Efficient base determination in sequencing reactions

ABSTRACT

The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of priority to U.S. PatentApplication Nos. 60/992,485, filed Dec. 5, 2007; 61/026,337, filed Feb.5, 2008; 61/035,914, filed Mar. 12, 2008; 61/061,134, filed Jun. 13,2008; 61/116,193, filed Nov. 19, 2008; 61/102,586, filed on Oct. 3,2008; 12/265,593, filed Nov. 5, 2008; and 12/266,385, filed Nov. 6,2008, each of which is hereby incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

Large-scale genomic sequence analysis is a key step toward understandinga wide range of biological phenomena. The need for low-cost,high-throughput sequencing and re-sequencing has led to the developmentof new approaches to sequencing that employ parallel analysis ofmultiple nucleic acid targets simultaneously.

Conventional methods of sequencing are generally restricted todetermining a few tens of nucleotides before signals becomesignificantly degraded, thus placing a significant limit on overallsequencing efficiency. Conventional methods of sequencing are also oftenlimited by signal-to-noise ratios that render such methods unsuitablefor single-molecule sequencing.

It would be advantageous for the field if methods and compositions couldbe designed to increase the efficiency of sequencing reactions as wellas the efficiency of assembling complete sequences from shorter readlengths.

SUMMARY OF THE INVENTION

Accordingly, the present invention provides methods and compositions forsequencing reactions.

In one aspect, the present invention provides a method for determining asequence in a target nucleic acid. This method includes the steps of:(a) providing a sequencing template that includes a fragment of thetarget nucleic acid and an adaptor that includes at least a first anchorsite; (b) hybridizing an anchor probe to the anchor site, and the anchorprobe includes a region complementary to the adaptor site and three ormore degenerate bases for binding in the target nucleic acid sequence;(c) hybridizing a pool of sequencing probes for determination of thesequence of one or more nucleotides in a defined position relative tothe adaptor, wherein the sequencing probe is detectably labeled toidentify the presence of a particular base; (d) ligating the anchorprobe and the sequencing probe; and (e) detecting the sequencing probe,thereby determining a sequence in the target nucleic acid.

In a further aspect, the invention provides a method of determining theidentification of a first nucleotide at a detection position of a targetsequence comprising a plurality of detection positions. This methodincludes the steps of: (a) providing a surface with a plurality ofconcatemers, wherein each concatemer includes a plurality of monomersand each monomer comprises: (i) a first target domain of the targetsequence comprising a first set of target detection positions; (ii) atleast a first adaptor comprising: (1) a first anchor site; and (2) asecond adjacent anchor site; (b) hybridizing a first anchor probe to thefirst anchor site; (c) hybridizing a second anchor probe to the secondanchor site, wherein the second anchor probe also hybridizes tosequences outside the second anchor site; (d) hybridizing at least afirst sequencing probe to the first target domain, wherein the firstsequencing probe comprises: (i) a first probe domain complementary tothe target domain; (ii) a unique nucleotide at a first interrogationposition; and (iii) a label; under conditions wherein if the uniquenucleotide is complementary to the first nucleotide, the sequencingprobe hybridizes to the concatemer; (e) ligating the anchor probes andthe sequencing probe; and (f) identifying the first nucleotide.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic illustration of an embodiment of a method forfragmenting nucleic acids.

FIG. 2 is a schematic illustration of embodiments of the inventionrelated to long fragment read (LFR) technology. FIG. 2A illustrates amethod for fragmenting nucleic acids by a standard multiple displacementamplification method (MDA). FIG. 2B illustrates a method for fragmentingnucleic acids by a multiple displacement amplification method utilizinga 5′ exonuclease. FIG. 2C is a schematic of an embodiment of the overallLFR process.

FIG. 3 is a schematic illustration of embodiments of a barcode adaptordesign for use in methods of the invention.

FIG. 4 is a schematic illustration of an embodiment of the invention forfragmenting nucleic acids utilizing a nick translation method.

FIG. 5 is a schematic illustration of adaptors that can be used inembodiments of the invention. FIG. 5A provides four different sequencesof adaptors. FIG. 5B illustrates different components that can beincluded in the design of an adaptor of the invention.

FIG. 6 is a schematic illustration of an embodiment of the invention formaking circular nucleic acid templates comprising multiple adaptors.

FIG. 7 is a schematic illustration of an embodiment of the invention forcontrolling the orientation of adaptors inserted into target nucleicacids.

FIG. 8 is a schematic illustration of exemplary embodiments of differentorientations in which adaptors and target nucleic acid molecules can beligated to each other.

FIG. 9 is a schematic illustration of one aspect of a method forassembling nucleic acid templates of the invention.

FIG. 10 is a schematic illustration of components of adaptors that areuseful for controlling the way such adaptors are inserted into a targetnucleic acid.

FIG. 11 is a schematic illustration of an embodiment of an arm-by-armligation process for inserting adaptors into target nucleic acids. FIG.11A illustrates an exemplary embodiment of the arm-by-arm ligationprocess and FIG. 11B illustrates exemplary components of adaptor arms ofuse in this process.

FIG. 12 is a schematic illustration of possible orientations of adaptorinsertion.

FIG. 13 is a schematic illustration of one embodiment of a nicktranslation ligation method.

FIG. 14 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 15 is a schematic illustration of one embodiment of a nicktranslation ligation method.

FIG. 16 is a schematic illustration of one embodiment of a nicktranslation ligation method.

FIG. 17 is a schematic illustration of one embodiment of a nicktranslation ligation method utilizing nick translation circle inversion(FIG. 17A) and nick translation circle inversion combined with uracildegradation (FIG. 17B).

FIG. 18 is a schematic illustration of an embodiment of a nicktranslation ligation method.

FIG. 19 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 20 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 21 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 22 is a schematic illustration of one embodiment of a method forinserting multiple adaptors.

FIG. 23 is a schematic illustration of one embodiment of a combinatorialprobe anchor ligation method.

FIG. 24 is a schematic illustration of one embodiment of a combinatorialprobe anchor ligation method.

FIG. 25 is a schematic illustration of one embodiment of a combinatorialprobe anchor ligation method.

FIG. 26 is a schematic illustration of one embodiment of a combinatorialprobe anchor ligation method.

FIG. 27 is a graph of fluorescent intensity levels achieved for eachbase at defined positions using a double combinatorial probe anchorligation method.

FIG. 28 is a graph of data fit scores obtained for interrogatedpositions using a combinatorial probe anchor ligation method.

FIG. 29 is a graph of fluorescent intensity levels obtained for a singlebase interrogation at different time points using a single and a doublecombinatorial probe anchor ligation method.

FIG. 30 is a graph of data fit scores obtained for a single baseinterrogation at different time points using a single combinatorialprobe anchor ligation method.

FIG. 31 is a graph of fluorescent intensity levels achieved fordifferent positions using a variety of second anchor probes in doublecombinatorial probe anchor ligation methods compared to a singlecombinatorial probe anchor ligation method.

FIG. 32 is a graph illustrating the data fit scores obtained fordifferent positions using a variety of second anchor probes in doublecombinatorial probe anchor ligation methods compared to a singlecombinatorial probe anchor ligation method.

FIG. 33 is a graph illustrating the fluorescent intensity levelsachieved for different positions using a variety of double combinatorialprobe anchor ligation methods compared to a single combinatorial probeanchor ligation method.

FIG. 34 is a graph illustrating data fit scores obtained for differentpositions using a variety of first anchor probes of different length ina double combinatorial probe anchor ligation method.

FIG. 35 is a graph illustrating the fluorescent intensity levelsachieved for each base at a defined position using a doublecombinatorial probe anchor ligation method in the presence of a kinaseat different temperatures.

FIG. 36 is a graph illustrating data fit scores obtained for a definedposition using a double combinatorial probe anchor ligation method inthe presence of a kinase at different temperatures.

FIG. 37 is a graph illustrating the fluorescent intensity levelsachieved for each base at a defined position using a doublecombinatorial probe anchor ligation method in the presence of a kinaseat different kinase incubation times.

FIG. 38 is a graph illustrating the data fit scores obtained for adefined position using a double combinatorial probe anchor ligationmethod in the presence of a kinase at different kinase incubation times.

DETAILED DESCRIPTION OF THE INVENTION

The practice of the present invention may employ, unless otherwiseindicated, conventional techniques and descriptions of organicchemistry, polymer technology, molecular biology (including recombinanttechniques), cell biology, biochemistry, and immunology, which arewithin the skill of the art. Such conventional techniques includepolymer array synthesis, hybridization, ligation, and detection ofhybridization using a label. Specific illustrations of suitabletechniques can be had by reference to the example herein below. However,other equivalent conventional procedures can, of course, also be used.Such conventional techniques and descriptions can be found in standardlaboratory manuals such as Genome Analysis: A Laboratory Manual Series(Vols. I-IV), Using Antibodies: A Laboratory Manual, Cells: A LaboratoryManual, PCR Primer: A Laboratory Manual, and Molecular Cloning: ALaboratory Manual (all from Cold Spring Harbor Laboratory Press),Stryer, L. (1995) Biochemistry (4th Ed.) Freeman, New York, Gait,“Oligonucleotide Synthesis: A Practical Approach” 1984, IRL Press,London, Nelson and Cox (2000), Lehninger, Principles of Biochemistry3^(rd) Ed., W. H. Freeman Pub., New York, N.Y. and Berg et al. (2002)Biochemistry, 5^(th) Ed., W. H. Freeman Pub., New York, N.Y., all ofwhich are herein incorporated in their entirety by reference for allpurposes.

Note that as used herein and in the appended claims, the singular forms“a,” “an,” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “a polymerase”refers to one agent or mixtures of such agents, and reference to “themethod” includes reference to equivalent steps and methods known tothose skilled in the art, and so forth.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. All publications mentionedherein are incorporated herein by reference for the purpose ofdescribing and disclosing devices, compositions, formulations andmethodologies which are described in the publication and which might beused in connection with the presently described invention.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly dictates otherwise, between the upper and lowerlimit of that range and any other stated or intervening value in thatstated range is encompassed within the invention. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges is also encompassed within the invention, subject to anyspecifically excluded limit in the stated range. Where the stated rangeincludes one or both of the limits, ranges excluding either both ofthose included limits are also included in the invention.

In the following description, numerous specific details are set forth toprovide a more thorough understanding of the present invention. However,it will be apparent to one of skill in the art that the presentinvention may be practiced without one or more of these specificdetails. In other instances, well-known features and procedures wellknown to those skilled in the art have not been described in order toavoid obscuring the invention.

Although the present invention is described primarily with reference tospecific embodiments, it is also envisioned that other embodiments willbecome apparent to those skilled in the art upon reading the presentdisclosure, and it is intended that such embodiments be contained withinthe present inventive methods.

I. Overview

The present invention is directed to compositions and methods fornucleic acid identification and detection, which find use in a widevariety of applications as described herein.

The overall method for sequencing target nucleic acids using thecompositions and methods of the present invention includes extractingand fragmenting target nucleic acids from a sample. The fragmentednucleic acids are used to produce target nucleic acid templates thatwill generally include one or more adaptors. The target nucleic acidtemplates are subjected to amplification methods to form nucleic acidnanoballs, which are usually disposed on a surface. Sequencingapplications are performed on the nucleic acid nanoballs of theinvention, usually through sequencing by ligation techniques, includingcombinatorial probe anchor ligation (“cPAL”) methods, which aredescribed in further detail below. cPAL and other sequencing methods canalso be used to detect specific sequences, such as including singlenucleotide polymorphisms (“SNPs”) in nucleic acid constructs of theinvention, (which include nucleic acid nanoballs as well as linear andcircular nucleic acid templates).

II. Preparing Fragments of Genomic Nucleic Acid

As discussed further herein, nucleic acid templates of the inventioncomprise target nucleic acids and adaptors. In order to obtain targetnucleic acids for construction of the nucleic acid templates of theinvention, the present invention provides methods for obtaining genomicnucleic acids from a sample and for fragmenting those genomic nucleicacids to produce fragments of use in subsequent methods for constructingnucleic acid templates of the invention.

IIA. Overview of Preparing Fragments of Genomic Nucleic Acid

Target nucleic acids can be obtained from a sample using methods knownin the art. As will be appreciated, the sample may comprise any numberof substances, including, but not limited to, bodily fluids (including,but not limited to, blood, urine, serum, lymph, saliva, anal and vaginalsecretions, perspiration and semen, of virtually any organism, withmammalian samples being preferred and human samples being particularlypreferred); environmental samples (including, but not limited to, air,agricultural, water and soil samples); biological warfare agent samples;research samples (i.e. in the case of nucleic acids, the sample may bethe products of an amplification reaction, including both target andsignal amplification as is generally described in PCT/US99/01705, suchas PCR amplification reaction); purified samples, such as purifiedgenomic DNA, RNA, proteins, etc.; raw samples (bacteria, virus, genomicDNA, etc.); as will be appreciated by those in the art, virtually anyexperimental manipulation may have been done on the sample. In oneaspect, the nucleic acid constructs of the invention are formed fromgenomic DNA. In certain embodiments, the genomic DNA is obtained fromwhole blood or cell preparations from blood or cell cultures.

In an exemplary embodiment, genomic DNA is isolated from a targetorganism. By “target organism” is meant an organism of interest and aswill be appreciated, this term encompasses any organism from whichnucleic acids can be obtained, particularly from mammals, includinghumans, although in some embodiments, the target organism is a pathogen(for example for the detection of bacterial or viral infections).Methods of obtaining nucleic acids from target organisms are well knownin the art. Samples comprising genomic DNA of humans find use in manyembodiments. In some aspects such as whole genome sequencing, about 20to about 1,000,0000 or more genome-equivalents of DNA are preferablyobtained to ensure that the population of target DNA fragmentssufficiently covers the entire genome. The number of genome equivalentsobtained may depend in part on the methods used to further preparefragments of the genomic DNA for use in accordance with the presentinvention. For example, in the long fragment read methods describedfurther below, about 20 to about 50 genome equivalents are generallyutilized. For methods utilizing multiple displacement amplification,which is also described further below, about 1000 to about 100,000genome equivalents are generally utilized. For methods in which noamplification is used prior to fragmenting, about 100,000 to about1,000,000 genome equivalents are used.

The target genomic DNA is isolated using conventional techniques, forexample as disclosed in Sambrook and Russell, Molecular Cloning: ALaboratory Manual, cited supra. The target genomic DNA is thenfractionated or fragmented to a desired size by conventional techniquesincluding enzymatic digestion, shearing, or sonication, with the lattertwo finding particular use in the present invention.

Fragment sizes of the target nucleic acid can vary depending on thesource target nucleic acid and the library construction methods used,but typically range from 50 to 600 nucleotides in length. In anotherembodiment, the fragments are 300 to 600 or 200 to 2000 nucleotides inlength. In yet another embodiment, the fragments are 10-100, 50-100,50-300, 100-200, 200-300, 50-400, 100-400, 200-400, 300-400, 400-500,400-600, 500-600, 50-1000, 100-1000, 200-1000, 300-1000, 400-1000,500-1000, 600-1000, 700-1000, 700-900, 700-800, 800-1000, 900-1000,1500-2000, 1750-2000, and 50-2000 nucleotides in length.

In a further embodiment, fragments of a particular size or in aparticular range of sizes are isolated. Such methods are well known inthe art. For example, gel fractionation can be used to produce apopulation of fragments of a particular size within a range ofbasepairs, for example for 500 base pairs±50 base pairs.

In many cases, enzymatic digestion of extracted DNA is not requiredbecause shear forces created during lysis and extraction will generatefragments in the desired range. In a further embodiment, shorterfragments (1-5 kb) can be generated by enzymatic fragmentation usingrestriction endonucleases. In a still further embodiment, about 10 toabout 1,000,000 genome-equivalents of DNA ensure that the population offragments covers the entire genome. Libraries containing nucleic acidtemplates generated from such a population of fragments will thuscomprise target nucleic acids whose sequences, once identified andassembled, will provide most or all of the sequence of an entire genome.

In some cases, it is advantageous to provide carrier DNA, e.g. unrelatedcircular synthetic double-stranded DNA, to be mixed and used with thesample DNA whenever only small amounts of sample DNA are available andthere is danger of losses through nonspecific binding, e.g. to containerwalls and the like.

In one embodiment, the DNA is denatured after fragmentation to producesingle stranded fragments.

In one embodiment, after fragmenting, (and in fact before or after anystep outlined herein) an amplification step can be applied to thepopulation of fragmented nucleic acids to ensure that a large enoughconcentration of all the fragments is available for subsequent steps ofcreating the decorated nucleic acids of the invention and using thosenucleic acids for obtaining sequence information. Such amplificationmethods are well known in the art and include without limitation:polymerase chain reaction (PCR), ligation chain reaction (sometimesreferred to as oligonucleotide ligase amplification OLA), cycling probetechnology (CPT), strand displacement assay (SDA), transcriptionmediated amplification (TMA), nucleic acid sequence based amplification(NASBA), rolling circle amplification (RCA) (for circularizedfragments), and invasive cleavage technology.

In further embodiments, after fragmenting, target nucleic acids arefurther modified to prepare them for insertion of multiple adaptorsaccording to methods of the invention. Such modifications can benecessary because the process of fragmentation may result in targetnucleic acids with termini that are not amenable to the procedures usedto insert adaptors, particularly the use of enzymes such as ligases andpolymerases. As for all the steps outlined herein, this step is optionaland can be combined with any step.

In an exemplary embodiment, after physical fragmenting, target nucleicacids frequently have a combination of blunt and overhang ends as wellas combinations of phosphate and hydroxyl chemistries at the termini. Inthis embodiment, the target nucleic acids are treated with severalenzymes to create blunt ends with particular chemistries. In oneembodiment, a polymerase and dNTPs is used to fill in any 5′ singlestrands of an overhang to create a blunt end. Polymerase with 3′exonuclease activity (generally but not always the same enzyme as the 5′active one, such as T4 polymerase) is used to remove 3′ overhangs.Suitable polymerases include, but are not limited to, T4 polymerase, Taqpolymerases, E. coli DNA Polymerase 1, Klenow fragment, reversetranscriptases, 029 related polymerases including wild type 029polymerase and derivatives of such polymerases, T7 DNA Polymerase, T5DNA Polymerase, RNA polymerases. These techniques can be used togenerate blunt ends, which are useful in a variety of applications.

In further optional embodiments, the chemistry at the termini is alteredto avoid target nucleic acids from ligating to each other. For example,in addition to a polymerase, a protein kinase can also be used in theprocess of creating blunt ends by utilizing its 3′ phosphatase activityto convert 3′ phosphate groups to hydroxyl groups. Such kinases caninclude without limitation commercially available kinases such as T4kinase, as well as kinases that are not commercially available but havethe desired activity.

Similarly, a phosphatase can be used to convert terminal phosphategroups to hydroxyl groups. Suitable phosphatases include, but are notlimited to, Alkaline Phosphatase (including Calf Intestinal (CIP)),Antarctic Phosphatase, Apyrase, Pyrophosphatase, Inorganic (yeast)thermostable inorganic pyrophosphatase, and the like, which are known inthe art and commercially available, for example from New EnglandBiolabs.

As depicted in FIG. 16, these modifications prevent the target nucleicacids from ligating to each other in later steps of methods of theinvention, thus ensuring that during steps in which adaptors (and/oradaptor arms) are ligated to the termini of target nucleic acids, targetnucleic acids will ligate to adaptors but not to other target nucleicacids. Target nucleic acids 1601 and 1602 are preferably ligated toadaptors 1603 and 1604 in a desired orientation (as illustrated in thisfigure, the desired orientation is one in which the ends with the sameshape—circle or square—ligates to each other). Modifying the ends avoidsthe undesired configurations 1607, 1608, 1609 and 1610, in which thetarget nucleic acids ligate to each other and the adaptors ligate toeach other. In addition, as will be discussed in further detail below,the orientation of each adaptor-target nucleic acid ligation can also becontrolled through control of the chemistry of the termini of both theadaptors and the target nucleic acids. The control over the chemistry ofthe termini can be provided using methods known in the art and describedfurther herein.

As will be appreciated by those in the art, and as for all the stepsoutlined herein, any combination of these steps and enzymes may be used.For example, some enzymatic fragmentation techniques, such as the use ofrestriction endonucleases, may render one or more of these enzymatic“end repair” steps superfluous.

The modifications described above can prevent the creation of nucleicacid templates containing different fragments ligated in an unknownconformation, thus reducing and/or removing the errors in sequenceidentification and assembly that can result from such undesiredtemplates.

In some cases, hierarchical fragmentation methods are utilized incombination with any of the enzymatic or mechanical methods offragmenting described herein. Such methods are described in U.S.application Ser. No. 11/451,692 and published PCT application WO2006/138284, which are herein incorporated by reference in theirentirety for all purposes and in particular for all teachings related tohierarchical fragmentation.

In some embodiments, a controlled random enzymatic (“CoRE”)fragmentation method is utilized to prepare fragments for use in theinvention. CoRE fragmentation is an enzymatic endpoint assay, and hasthe advantages of enzymatic fragmentation (such as the ability to use iton low amounts and/or volumes of DNA) without many of its drawbacks(including sensitivity to variation in substrate or enzyme concentrationand sensitivity to digestion time). Briefly, CoRE fragmentation involvesa series of three enzymatic steps, which are schematically illustrate inFIG. 1. First, a nucleic acid 101 is subjected to an enzyme catalyzedmultiple displacement amplification (MDA) in the presence of dNTPs dopedwith dUTP or UTP in a defined ration to the dTTP. This results in thesubstitution of deoxyuracil (“dU”) or uracil (“U”) at defined andcontrollable proportions of the T positions in both strands of theamplification product (103). The U moieties are then excised (104),usually through a combination of UDG, EndoVIII, and T4PNK, to createsingle base gaps with functional 5′ phosphate and 3′ hydroxyl ends(105). The single base gaps will be created at an average spacingdefined by the frequency of U in the MDA product. Treatment of thegapped nucleic acid (105) with a polymerase results in nick translationuntil nicks on opposite strands converge, thereby creating double strandbreaks, resulting a relatively population of double stranded fragmentsof a relatively homogenous size (107). Since the size distribution ofthe double stranded fragments (107) is a result of the ration of dTTP toDUTP or UTP used in the MDA reaction, rather than by the duration ordegree of enzymatic treatment, this CoRE fragmentation methods produceshigh degrees of fragmentation reproducibility.

In some cases, particularly when it is desired to isolate long fragments(such as fragments from about 150 to about 750 kilobases in length), thepresent invention provides methods in which cells are lysed and theintact nucleic are pelleted with a gentle centrifugation step. Thegenomic nucleic acid, usually genomic DNA, is released through enzymaticdigestion, using for example proteinase K and RNase digestion overseveral hours. The resultant material is then dialyzed overnight ordiluted directly to lower the concentration of remaining cellular waste.Since such methods of isolating the nucleic acid does not involve manydisruptive processes (such as ethanol precipitation, centrifugation, andvortexing), the genomic nucleic acid remains largely intact, yielding amajority of fragments in excess of 150 kilobases.

In some cases, in combination with any of the above-describedfragmentation methods, the present invention further provides methods ofaliquoting a population of genomic nucleic acid fragments which allowsthe reconstruction of diploid genomes, e.g. the identification ofmaternal and paternal chromosomes or sequence. This is a significantadvantage over the processes of the prior art.

In this embodiment, the genomic fragments are aliqoted such that thenucleic acids are diluted to a concentration of approximately 10% of ahaploid genome per aliquot. At such a level of dilution, approximately95% of the base pairs in a particular aliquot are non-overlapping. Thismethod of aliquoting, also referred to herein as a long fragment read(LFR) fragmentation method, can in particular embodiments be used onlarge molecular weight fragments isolated according to the methodsdescribed above and further herein. An example of an LFR method isschematically illustrated in FIG. 2C. LFR usually begins with a shorttreatment of genomic nucleic acids, usually genomic DNA, with a 5′exonuclease to create 3′ single-stranded overhangs. Such single strandedoverhangs serve as multiple displacement amplification (MDA) initiationsites (FIG. 2A). The 5′ exonuclease treated DNA is then diluted tosub-genome concentrations and dispersed across a number of aliquots,usually across a number of wells in a multiwell plate. The fragments ineach well are amplified, usually using a standard MDA method (FIG. 2A)and/or an MDA method utilizing an exonuclease (FIG. 2B). In some cases,the amplification method introduces uracil moieties into the fragments,such that the above-described CoRE method can be used to furtherfragment the fragments in each well following amplification. Thefragmenting of the MDA products can also be achieved via sonication orenzymatic treatment. In general, following fragmentation of the MDAproducts, the ends of the resultant fragments are repaired, usually withT4 polymerase and T4 polynucleotide kinase. Fragments are then treatedwith alkaline phosphatase and then the fragments are tagged with anadaptor. Generally, the tag adaptor arm is designed in two segments—onesegment is common to all wells and blunt end ligates directly to thefragments using methods described further herein. The second segment isunique to each well and contains a “barcode” sequence such that when thecontents of each well are combined, the fragments from each well can beidentified. FIG. 3 illustrates some exemplary barcode adaptors that canbe added to the fragments for this aspect of the invention.

In some cases, an LFR method is used to analyze the genome of anindividual cell. The process for isolating DNA in this case is similarto the methods described above, but occurs in a smaller volume. Once theDNA is isolated and before it is aliquoted into individual wells, thegenomic DNA must be carefully fragmented to avoid loss of material,particularly to avoid loss of sequence from the ends of each fragment,since loss of such material will result in gaps in the final genomeassembly. In some cases, sequence loss is avoided through use of aninfrequent nicking enzyme, which creates starting sites for apolymerase, such as phi29 polymerase, at distances of approximately 100kb from each other. As the polymerase creates the new DNA strand, itdisplaces the old strand, with the end result being that there areoverlapping sequences near the sites of polymerase initiation (FIG. 4),resulting in very few deletions of sequence.

In some cases, it is advantageous to provide carrier DNA, e.g. unrelatedcircular synthetic double-stranded DNA, to be mixed and used with thesample DNA whenever only small amounts of sample DNA are available andthere is danger of losses through nonspecific binding, e.g. to containerwalls and the like. In one embodiment, the DNA is denatured afterfragmentation to produce single stranded fragments.

In one embodiment, after fragmenting, (and in fact before or after anystep outlined herein) an amplification step can be applied to thepopulation of fragmented nucleic acids to ensure that a large enoughconcentration of all the fragments is available for subsequent steps ofcreating the decorated nucleic acids of the invention and using thosenucleic acids for obtaining sequence information. Such amplificationmethods are well known in the art and include without limitation:polymerase chain reaction (PCR), ligation chain reaction (sometimesreferred to as oligonucleotide ligase amplification OLA), cycling probetechnology (CPT), strand displacement assay (SDA), transcriptionmediated amplification (TMA), nucleic acid sequence based amplification(NASBA), rolling circle amplification (RCA) (for circularizedfragments), and invasive cleavage technology.

In further embodiments, after fragmenting, target nucleic acids arefurther modified to prepare them for insertion of multiple adaptorsaccording to methods of the invention. Such modifications can benecessary because the process of fragmentation may result in targetnucleic acids with termini that are not amenable to the procedures usedto insert adaptors, particularly the use of enzymes such as ligases andpolymerases. As for all the steps outlined herein, this step is optionaland can be combined with any step. Methods for modifying the fragmentsto prepare them for directed ligation to other nucleic acid moleculesinclude application of enzymes, such as polymerases and phosphatases, tomodify the ends of the fragments such that they are only able to ligateto other nucleic acid molecules in a desired orientation. Such methodsare described further herein.

IIB. CoRE Fragmentation

As discussed above, methods of fragmentation for use in the presentinvention include both mechanical and enzymatic fragmentation methods,as well as combinations of enzymatic and fragmentation methods. Manymechanical and enzymatic fragmentation methods are well known in theart.

In one aspect, the present invention provides a method of fragmentationreferred to herein as Controlled Random Enzymatic (CoRE) fragmentation.The CoRE fragmentation methods described herein can be used alone or incombination with other mechanical and enzymatic fragmentation methodsknown in the art. CoRE fragmentation involves a series of threeenzymatic steps, which are schematically illustrated in FIG. 1. First, anucleic acid 101 is subjected to an amplification method that isconducted in the present of dNTPs doped with a proportion of deoxyuracil(“dU”) or uracil (“U”) to result in substitution of dUTP or UTP atdefined and controllable proportions of the T positions in both strandsof the amplification product (103). A number of amplification methodscan be used in this step of the invention, including without limitationpolymerase chain reaction (PCR), ligation chain reaction (sometimesreferred to as oligonucleotide ligase amplification OLA), cycling probetechnology (CPT), strand displacement assay (SDA), transcriptionmediated amplification (TMA), nucleic acid sequence based amplification(NASBA), rolling circle amplification (RCA) (for circularizedfragments), and invasive cleavage technology. In certain embodiment,multiple displacement amplification (MDA) in the presence of dNTPs dopedwith dUTP or UTP in a defined ratio to the dTTP is used to createamplification products with dUTP or UTP substituted into certain pointson both strands (103).

After amplification and insertion of the uracil moieties, the uracilsare then excised (104), usually through a combination of UDG, EndoVIll,and T4PNK, to create single base gaps with functional 5′ phosphate and3′ hydroxyl ends (105). The single base gaps will be created at anaverage spacing defined by the frequency of U in the MDA product. Thatis, the higher the amount of dUTP, the shorter the resulting fragments.As will be appreciated by those in the art, other techniques that willresult in selective replacement of a nucleotide with a modifiednucleotide that can similarly result in cleavage can also be used, suchas chemically or other enzymatically susceptible nucleotides.

Treatment of the gapped nucleic acid (105) with a polymerase withexonuclease activity results in “translation” or “translocation” of thenicks along the length of the nucleic acid until nicks on oppositestrands converge, thereby creating double strand breaks, resulting arelatively population of double stranded fragments of a relativelyhomogenous size (107). The exonuclease activity of the polymerase (suchas Taq polymerase) will excise the short DNA strand that abuts the nickwhile the polymerase activity will “fill in” the nick and subsequentnucleotides in that strand (essentially, the Taq moves along the strand,excising bases using the exonuclease activity and adding the same bases,with the result being that the nick is translocated along the stranduntil the enzyme reaches the end).

Since the size distribution of the double stranded fragments (107) is aresult of the ration of dTTP to DUTP or UTP used in the MDA reaction,rather than by the duration or degree of enzymatic treatment, this CoREfragmentation methods produces high degrees of fragmentationreproducibility. Thus, CoRE fragmentation results in a population ofdouble stranded nucleic acid fragments that are all of a similar size.

IIC. Long Fragment Read Technology

Long Fragment Read (LFR) methods of the invention are based on thephysical separation of long genomic DNA fragments across many differentaliquots such that the probability of any given region of the genome ofboth the maternal and paternal component in the same aliquot is veryrare. By placing a unique identifier in each aliquot and analyzing manyaliquot in the aggregate, long fragments of DNA can be assembled into adiploid genome, e.g. the sequence of each parental chromosome can beprovided, providing a significant advantage over the prior art. Whilethe discussion herein focuses on the use of the LFR methods using DNBarrays and sequencing by ligation, it should be appreciated that theseLFR methods can be used with a variety of other arrays and othersequencing methods to result in the sequencing of diploid genomes as twoseparate haploid genomes. This can facilitate the identification offamilial genetic disease, etc.

To achieve an appropriate separation of fragments, in general the DNA isdiluted to a concentration of approximately 10% of a haploid genome peraliquot (FIG. 2C). At this concentration, 95% of the base pairs in analiquot are non-overlapping. Such a dilution results in a statisticalseparation such that maternal and paternal fragments will usually landin different aliquots (FIG. 2C, second panel). It should be appreciatedthat the dilution factor can depend on the original size of thefragments. That is, using gentle techniques to isolate genomic DNA,fragments of roughly 100 kb can be obtained, which are then aliquoted.Techniques that allow larger fragments result in a need for feweraliquots, and those that result in shorter fragments may require moredilution.

In some embodiments, the fragments in each aliquot are amplified and infurther embodiments the fragments in each aliquot are further fragmentedand then tagged with an adaptor such that fragments from the samealiquot will all comprise the same tag adaptor; see for example US2007/0072208, hereby incorporated by reference in its entirety, and inparticular for the discussions of additional aliquoting and coverage.

In many embodiments, each aliquot is contained in a separate well of amulti-well plate (for example, a 384 well plate). It will be appreciatedthat although the following discussion of LFR is provided in terms of amulti-well plate, that any number of different types of containers andsystems can be used to hold the different aliquots generated in thismethod. Such containers and systems are well known in the art and itwould be apparent to one of skill in the art what types of containersand systems would be appropriate to use in accordance with this aspectof the invention.

As discussed above, isolating long fragments of genomic nucleic acidfrom a cell can be accomplished by a number of different methods. In oneembodiment, cells are lysed and the intact nucleic are pelleted with agentle centrifugation step. The genomic DNA is then released throughproteinase K and RNase digestion for several hours. The material canthen in some embodiments be treated to lower the concentration ofremaining cellular waste—such treatments are well known in the art andcan include without limitation dialysis for a period of time (i.e., from2-16 hours) and/or dilution. Since such methods of isolating the nucleicacid does not involve many disruptive processes (such as ethanolprecipitation, centrifugation, and vortexing), the genomic nucleic acidremains largely intact, yielding a majority of fragments that havelengths in excess of 150 kilobases. In some embodiments, the fragmentsare from about 100 to about 750 kilobases in lengths. In furtherembodiments, the fragments are from about 150 to about 600, about 200 toabout 500, about 250 to about 400, and about 300 to about 350 kilobasesin length.

An example of an LFR method is schematically illustrated in FIG. 2. LFRusually begins with a short treatment of genomic nucleic acids, usuallygenomic DNA, with a 5′ exonuclease to create 3′ single-strandedoverhangs. Such single stranded overhangs serve as MDA initiation sites(FIG. 2). The use of the exonuclease also eliminates the need for a heator alkaline denaturation step prior to amplification without introducingbias into the population of fragments. In some embodiments, alkalinedenaturation is combined with the 5′ exonuclease treatment, whichresults in a reduction in bias that is greater than what is seen witheither treatment alone.

The DNA treated with the 5′ exonuclease and optionally the alkalinedenaturation is then diluted to sub-genome concentrations and dispersedacross a number of aliquots, usually across a number of wells in amultiwell plate. In some embodiments, a 10% genome equivalent isaliquoted into each well of a multiwell plate. If a 384 well plate isused, a 10% genome equivalent aliquot into each well results in eachplate comprising 38 genomes in total. In further embodiments, a 5-50%genome equivalent is aliquoted into each well. As noted above, thenumber of aliquots and genome equivalents can depend on the originalfragment size.

After separation across multiple wells, the fragments in each well areamplified, usually using an MDA method. In certain embodiments, the MDAreaction is a modified Phi29 polymerase-based amplification reaction.Although much of the discussion herein is in terms of an MDA reaction,it will be appreciated by those of skill in the art that many differentkinds of amplification reactions can be used in accordance with thepresent invention, and that such amplification reactions are well knownin the art and described generally in Maniatis et al., MolecularCloning: A Laboratory Manual, 2d Edition, 1989, and Short Protocols inMolecular Biology, ed. Ausubel, et al, hereby incorporated by reference.

In some embodiments, the MDA reaction is designed to introduce uracilsinto the amplification products. In some embodiments, a standard MDAreaction utilizing random hexamers is used to amplify the fragments ineach well. In many embodiments, rather than the random hexamers, random8-mer primers are used to reduce amplification bias in the population offragments. In further embodiments, several different enzymes can also beadded to the MDA reaction to reduce the bias of the amplification. Forexample, low concentrations of non-processive 5′ exonucleases and/orsingle-stranded binding proteins can be used to create binding sites forthe 8-mers. Chemical agents such as betaine, DMSO, and trehalose canalso be used to reduce bias through similar mechanisms.

After amplification of the fragments in each well, the amplificationproducts are then in many embodiments subjected to another round offragmentation. In some embodiments the above-described CoRE method isused to further fragment the fragments in each well followingamplification. As discussed above, in order to use the CoRE method, theMDA reaction used to amplify the fragments in each well is designed toincorporate uracils into the MDA products. The fragmenting of the MDAproducts can also be achieved via sonication or enzymatic treatment.Enzymatic treatment that could be used in this embodiment includes theuse of without limitation DNase I, T7 endonuclease I, Micrococcalnuclease, and the like.

In some embodiments, when a CoRE method is used to fragment the MDAproducts, each well containing MDA products are treated with a mix ofUracil DNA glycosylase (UDG), DNA glycosylase-lyase Endonuclease VIII,and T4 polynucleotide kinase to excise the uracil bases and createsingle base gaps with functional 5′ phosphate and 3′ hydroxyl groups.Nick translation through use of a polymerase such as Taq polymeraseresults in double stranded blunt end breaks, resulting in ligatablefragments of a size range dependent on the concentration of dUTP addedin the MDA reaction. In some embodiments, the CoRE method used involvesremoving uracils by polymerization and strand displacement by phi29 (seeFIG. 4).

In general, following fragmentation of the MDA products, the ends of theresultant fragments are repaired. Such repairs can be necessary, becausemany fragmentation techniques can result in termini with overhangingends and termini with functional groups that are not useful in laterligation reactions, such as 3′ and 5′ hydroxyl groups and/or 3′ and 5′phosphate groups. In many aspects of the present invention, it is usefulto have fragments that are repaired to have blunt ends, and in somecases, it can be desirable to alter the chemistry of the termini suchthat the correct orientation of phosphate and hydroxyl groups is notpresent, thus preventing “polymerization” of the target sequences. Thecontrol over the chemistry of the termini can be provided using methodsknown in the art. For example, in some circumstances, the use ofphosphatase eliminates all the phosphate groups, such that all endscontain hydroxyl groups. Each end can then be selectively altered toallow ligation between the desired components. One end of the fragmentscan then be “activated”, in some embodiments by treatment with alkalinephosphatase. The fragments are then in many embodiments tagged with anadaptor. In general, these tag adaptors can be used to identifyfragments that come from the same well in the LFR method.

FIG. 3 provides a schematic illustration of some embodiments of adaptordesign for use as a tag in accordance with the LFR method. Generally,the adaptor is designed in two segments—one segment is common to allwells and blunt end ligates directly to the fragments using methodsdescribed further herein. In the embodiment pictured in FIG. 3, the“common” adaptor is added as two adaptor arms—one arm is blunt endligated to the 5′ end of the fragment and the other arm is blunt endligated to the 3′ end of the fragment. The second segment of the taggingadaptor is a “barcode” segment that is unique to each well. This barcodeis generally a unique sequence of nucleotides, and each fragment in aparticular well is given the same barcode. Thus, when the taggedfragments from all the wells are re-combined for sequencingapplications, fragments from the same well can be identified throughidentification of the barcode adaptor. In the embodiment illustrated inFIG. 3, the barcode is ligated to the 5′ end of the common adaptor arm.The common adaptor and the barcode adaptor can be ligated to thefragment sequentially or simultaneously. As will be described in furtherdetail herein, the ends of the common adaptor and the barcode adaptorcan be modified such that each adaptor segment will ligate in thecorrect orientation and to the proper molecule. Such modificationsprevent “polymerization” of the adaptor segments or the fragments byensuring that the fragments are unable to ligate to each other and thatthe adaptor segments are only able to ligate in the illustratedorientation.

In further embodiments, a three segment design is utilized for theadaptors used to tag fragments in each well. This embodiment is similarto the barcode adaptor design described above, except that the barcodeadaptor segment is split into two segments (see FIG. 3). This designallows for a wider range of possible barcodes by allowing combinatorialbarcode adaptor segments to be generated by ligating different barcodesegments together to form the full barcode segment. This combinatorialdesign provides a larger repertoire of possible barcode adaptors whilereducing the number of full size barcode adaptors that need to begenerated.

After the fragments in each well are tagged, all of the fragments arecombined to form a single population. These fragments can then be usedto generate nucleic acid templates of the invention, as is discussed infurther detail below. The nucleic acid templates generated from thesetagged fragments will be identifiable as belonging to a particular wellby the barcode tag adaptors attached to each fragment.

In some cases, an LFR method is used to analyze the genome of a smallnumber of cells, including an individual cell. The process for isolatingDNA in this case is similar to the methods described above, but occursin a smaller volume. Once the DNA is isolated and before the step ofaliquoting the sample into individual wells, the genomic DNA must becarefully fragmented to avoid loss of material, particularly to avoidloss of sequence from the ends of each fragment, since loss of suchmaterial will result in gaps in the final genome assembly. In somecases, sequence loss is avoided through use of an infrequent nickingenzyme, which creates starting sites for a polymerase, such as phi29polymerase, at distances of approximately 100 kb from each other. As thepolymerase creates the new DNA strand, it displaces the old strand, withthe end result being that there are overlapping sequences near the sitesof polymerase initiation (FIG. 4), resulting in very few deletions ofsequence. In a further embodiment, the DNA can then be diluted andaliquoted into multiple wells following the methods described above. Insome embodiments, a controlled use of a 5′ exonuclease (either before orduring the MDA reaction) can promote multiple replications of theoriginal DNA from the single cell and thus minimize propagation of earlyerrors through copying of copies.

It will be appreciated that the LFR methods described herein can be usedfor sequencing diploid genomes using any sequencing methods known in theart. The LFR methods described herein may in further embodiments be usedon any number of sequencing platforms, including for example withoutlimitation: GeneChip (Affymetrix), CodeLink Bioarray (Amersham),Expression Array System (Applied Biosystems), SurePrint microarrays(Agilent), Sentrix LD BeadChip or Sentrix Array Matrix (Illumine) andVerigene (Nanosphere).

In some embodiments, LFR methods described herein do not includemultiple levels or tiers of fragmentation/aliquoting, as described inU.S. patent application Ser. No. 11/451,692, filed Jun. 13, 2006, whichis herein incorporated by reference in its entirety for all purposes andin particular for all teachings related to methods of fragmenting andaliquoting nucleic acids. That is, some embodiments utilize only asingle round of aliquoting, and also allow the repooling of aliquots fora single array, rather than using separate arrays for each aliquot.

III. Nucleic Acid Templates of the Invention

The present invention provides nucleic acid template comprising targetnucleic acids and multiple interspersed adaptors. The nucleic acidtemplate constructs are assembled by inserting adaptors molecules at amultiplicity of sites throughout each target nucleic acid. Theinterspersed adaptors permit acquisition of sequence information frommultiple sites in the target nucleic acid consecutively orsimultaneously.

The term “target nucleic acid” refers to a nucleic acid of interest. Inone aspect, target nucleic acids of the invention are genomic nucleicacids, although other target nucleic acids can be used, including mRNA(and corresponding cDNAs, etc.). Target nucleic acids include naturallyoccurring or genetically altered or synthetically prepared nucleic acids(such as genomic DNA from a mammalian disease model). Target nucleicacids can be obtained from virtually any source and can be preparedusing methods known in the art. For example, target nucleic acids can bedirectly isolated without amplification, isolated by amplification usingmethods known in the art, including without limitation polymerase chainreaction (PCR), strand displacement amplification (SDA), multipledisplacement amplification (MDA), rolling circle amplification (RCA),rolling circle amplification (RCR) and other amplificationmethodologies. Target nucleic acids may also be obtained throughcloning, including but not limited to cloning into vehicles such asplasmids, yeast, and bacterial artificial chromosomes.

In some aspects, the target nucleic acids comprise mRNAs or cDNAs. Incertain embodiments, the target DNA is created using isolatedtranscripts from a biological sample. Isolated mRNA may be reversetranscribed into cDNAs using conventional techniques, again as describedin Genome Analysis: A Laboratory Manual Series (Vols. I-IV) or MolecularCloning: A Laboratory Manual.

The target nucleic acids may be single stranded or double stranded, asspecified, or contain portions of both double stranded or singlestranded sequence. Depending on the application, the nucleic acids maybe DNA (including genomic and cDNA), RNA (including mRNA and rRNA) or ahybrid, where the nucleic acid contains any combination of deoxyribo-and ribo-nucleotides, and any combination of bases, including uracil,adenine, thymine, cytosine, guanine, inosine, xathanine hypoxathanine,isocytosine, isoguanine, etc.

By “nucleic acid” or “oligonucleotide” or “polynucleotide” orgrammatical equivalents herein means at least two nucleotides covalentlylinked together. A nucleic acid of the present invention will generallycontain phosphodiester bonds, although in some cases, as outlined below(for example in the construction of primers and probes such as labelprobes), nucleic acid analogs are included that may have alternatebackbones, comprising, for example, phosphoramide (Beaucage et al.,Tetrahedron 49(10):1925 (1993) and references therein; Letsinger, J.Org. Chem. 35:3800 (1970); Sprinzl et al., Eur. J. Biochem. 81:579(1977); Letsinger et al., Nucl. Acids Res. 14:3487 (1986); Sawai et al,Chem. Lett. 805 (1984), Letsinger et al., J. Am. Chem. Soc. 110:4470(1988); and Pauwels et al., Chemica Scripta 26:141 91986)),phosphorothioate (Mag et al., Nucleic Acids Res. 19:1437 (1991); andU.S. Pat. No. 5,644,048), phosphorodithioate (Briu et al., J. Am. Chem.Soc. 111:2321 (1989), O-methylphosphoroamidite linkages (see Eckstein,Oligonucleotides and Analogues: A Practical Approach, Oxford UniversityPress), and peptide nucleic acid (also referred to herein as “PNA”)backbones and linkages (see Egholm, J. Am. Chem. Soc. 114:1895 (1992);Meier et al., Chem. Int. Ed. Engl. 31:1008 (1992); Nielsen, Nature,365:566 (1993); Carlsson et al., Nature 380:207 (1996), all of which areincorporated by reference). Other analog nucleic acids include thosewith bicyclic structures including locked nucleic acids (also referredto herein as “LNA”), Koshkin et al., J. Am. Chem. Soc. 120:13252 3(1998); positive backbones (Denpcy et al., Proc. Natl. Acad. Sci. USA92:6097 (1995); non-ionic backbones (U.S. Pat. Nos. 5,386,023,5,637,684, 5,602,240, 5,216,141 and 4,469,863; Kiedrowshi et al., Angew.Chem. Intl. Ed. English 30:423 (1991); Letsinger et al., J. Am. Chem.Soc. 110:4470 (1988); Letsinger et al., Nucleoside & Nucleotide 13:1597(1994); Chapters 2 and 3, ASC Symposium Series 580, “CarbohydrateModifications in Antisense Research”, Ed. Y. S. Sanghui and P. Dan Cook;Mesmaeker et al., Bioorganic & Medicinal Chem. Lett. 4:395 (1994); Jeffset al., J. Biomolecular NMR 34:17 (1994); Tetrahedron Lett. 37:743(1996)) and non-ribose backbones, including those described in U.S. Pat.Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series580, “Carbohydrate Modifications in Antisense Research”, Ed. Y. S.Sanghui and P. Dan Cook. Nucleic acids containing one or morecarbocyclic sugars are also included within the definition of nucleicacids (see Jenkins et al., Chem. Soc. Rev. (1995) pp 169 176). Severalnucleic acid analogs are described in Rawls, C & E News Jun. 2, 1997page 35. “Locked nucleic acids” (LNA™) are also included within thedefinition of nucleic acid analogs. LNAs are a class of nucleic acidanalogues in which the ribose ring is “locked” by a methylene bridgeconnecting the 2′-O atom with the 4′-C atom. All of these references arehereby expressly incorporated by reference in their entirety for allpurposes and in particular for all teachings related to nucleic acids.These modifications of the ribose-phosphate backbone may be done toincrease the stability and half-life of such molecules in physiologicalenvironments. For example, PNA:DNA and LNA-DNA hybrids can exhibithigher stability and thus may be used in some embodiments.

The nucleic acid templates (also referred to herein as “nucleic acidconstructs” and “library constructs”) of the invention comprise targetnucleic acids and adaptors. As used herein, the term “adaptor” refers toan oligonucleotide of known sequence. Adaptors of use in the presentinvention may include a number of elements. The types and numbers ofelements (also referred to herein as “features”) included in an adaptorwill depend on the intended use of the adaptor. Adaptors of use in thepresent invention will generally include without limitation sites forrestriction endonuclease recognition and/or cutting, particularly TypeIIs recognition sites that allow for endonuclease binding at arecognition site within the adaptor and cutting outside the adaptor asdescribed below, sites for primer binding (for amplifying the nucleicacid constructs) or anchor primer (sometimes also referred to herein as“anchor probes”) binding (for sequencing the target nucleic acids in thenucleic acid constructs), nickase sites, and the like. In someembodiments, adaptors will comprise a single recognition site for arestriction endonuclease, whereas in other embodiments, adaptors willcomprise two or more recognition sites for one or more restrictionendonucleases. As outlined herein, the recognition sites are frequently(but not exclusively) found at the termini of the adaptors, to allowcleavage of the double stranded constructs at the farthest possibleposition from the end of the adaptor.

In some embodiments, adaptors of the invention have a length of about 10to about 250 nucleotides, depending on the number and size of thefeatures included in the adaptors. In certain embodiments, adaptors ofthe invention have a length of about 50 nucleotides. In furtherembodiments, adaptors of use in the present invention have a length ofabout 20 to about 225, about 30 to about 200, about 40 to about 175,about 50 to about 150, about 60 to about 125, about 70 to about 100, andabout 80 to about 90 nucleotides.

In further embodiments, adaptors may optionally include elements suchthat they can be ligated to a target nucleic acid as two “arms”. One orboth of these arms may comprise an intact recognition site for arestriction endonuclease, or both arms may comprise part of arecognition site for a restriction endonuclease. In the latter case,circularization of a construct comprising a target nucleic acid boundedat each termini by an adaptor arm will reconstitute the entirerecognition site.

In still further embodiments, adaptors of use in the invention willcomprise different anchor binding sites at their 5′ and the 3′ ends ofthe adaptor. As described further herein, such anchor binding sites canbe used in sequencing applications, including the combinatorial probeanchor ligation (cPAL) method of sequencing, described herein and inU.S. Application Nos. 60/992,485; 61/026,337; 61/035,914; 61/061,134;61/116,193; 61/102,586; 12/265,593; and 12/266,385 11/938,106;11/938,096; 11/982,467; 11/981,804; 11/981,797; 11/981,793; 11/981,767;11/981,761; 11/981,730; 11/981,685; 11/981,661; 11/981,607; 11/981,605;11/927,388; 11/927,356; 11/679,124; 11/541,225; 10/547,214; and11/451,691, all of which are hereby incorporated by reference in theirentirety, and particularly for disclosure relating to sequencing byligation.

In one aspect, adaptors of the invention are interspersed adaptors. By“interspersed adaptors” is meant herein oligonucleotides that areinserted at spaced locations within the interior region of a targetnucleic acid. In one aspect, “interior” in reference to a target nucleicacid means a site internal to a target nucleic acid prior to processing,such as circularization and cleavage, that may introduce sequenceinversions, or like transformations, which disrupt the ordering ofnucleotides within a target nucleic acid.

The nucleic acid template constructs of the invention contain multipleinterspersed adaptors inserted into a target nucleic acid, and in aparticular orientation. As discussed further herein, the target nucleicacids are produced from nucleic acids isolated from one or more cells,including one to several million cells. These nucleic acids are thenfragmented using mechanical or enzymatic methods.

The target nucleic acid that becomes part of a nucleic acid templateconstruct of the invention may have interspersed adaptors inserted atintervals within a contiguous region of the target nucleic acids atpredetermined positions. The intervals may or may not be equal. In someaspects, the accuracy of the spacing between interspersed adaptors maybe known only to an accuracy of one to a few nucleotides. In otheraspects, the spacing of the adaptors is known, and the orientation ofeach adaptor relative to other adaptors in the library constructs isknown. That is, in many embodiments, the adaptors are inserted at knowndistances, such that the target sequence on one termini is contiguous inthe naturally occurring genomic sequence with the target sequence on theother termini. For example, in the case of a Type IIs restrictionendonuclease that cuts 16 bases from the recognition site, located 3bases into the adaptor, the endonuclease cuts 13 bases from the end ofthe adaptor. Upon the insertion of a second adaptor, the target sequence“upstream” of the adaptor and the target sequence “downstream” of theadaptor are actually contiguous sequences in the original targetsequence.

Although the embodiments of the invention described herein are generallydescribed in terms of circular nucleic acid template constructs, it willbe appreciated that nucleic acid template constructs may also be linear.Furthermore, nucleic acid template constructs of the invention may besingle- or double-stranded, with the latter being preferred in someembodiments

The present invention provides nucleic acid templates comprising atarget nucleic acid containing one or more interspersed adaptors. In afurther embodiment, nucleic acid templates formed from a plurality ofgenomic fragments can be used to create a library of nucleic acidtemplates. Such libraries of nucleic acid templates will in someembodiments encompass target nucleic acids that together encompass allor part of an entire genome. That is, by using a sufficient number ofstarting genomes (e.g. cells), combined with random fragmentation, theresulting target nucleic acids of a particular size that are used tocreate the circular templates of the invention sufficiently “cover” thegenome, although as will be appreciated, on occasion, bias may beintroduced inadvertently to prevent the entire genome from beingrepresented.

The nucleic acid template constructs of the invention comprise multipleinterspersed adaptors, and in some aspects, these interspersed adaptorscomprise one or more recognition sites for restriction endonucleases. Infurther aspect, the adaptors comprise recognition sites for Type IIsendonucleases. Type-IIs endonucleases are generally commerciallyavailable and are well known in the art. Like their Type-IIcounterparts, Type-IIs endonucleases recognize specific sequences ofnucleotide base pairs within a double stranded polynucleotide sequence.Upon recognizing that sequence, the endonuclease will cleave thepolynucleotide sequence, generally leaving an overhang of one strand ofthe sequence, or “sticky end.” Type-IIs endonucleases also generallycleave outside of their recognition sites; the distance may be anywherefrom about 2 to 30 nucleotides away from the recognition site dependingon the particular endonuclease. Some Type-IIs endonucleases are “exactcutters” that cut a known number of bases away from their recognitionsites. In some embodiments, Type IIs endonucleases are used that are not“exact cutters” but rather cut within a particular range (e.g. 6 to 8nucleotides). Generally, Type IIs restriction endonucleases of use inthe present invention have cleavage sites that are separated from theirrecognition sites by at least six nucleotides (i.e. the number ofnucleotides between the end of the recognition site and the closestcleavage point). Exemplary Type IIs restriction endonucleases include,but are not limited to, Eco57M I, Mme I, Acu I, Bpm I, BceA I, Bbv I,BciV I, BpuE I, BseM II, BseR I, Bsg I, BsmF I, BtgZ I, Eci I, EcoP15 I,Eco57M I, Fok I, Hga I, Hph I, Mbo II, Mnl I, SfaN I, TspDT I, TspDW I,Taq II, and the like. In some exemplary embodiments, the Type IIsrestriction endonucleases used in the present invention are AcuI, whichhas a cut length of about 16 bases with a 2-base 3′ overhang and EcoP15,which has a cut length of about 25 bases with a 2-base 5′ overhang. Aswill be discussed further below, the inclusion of a Type IIs site in theadaptors of the nucleic acid template constructs of the inventionprovides a tool for inserting multiple adaptors in a target nucleic acidat a defined location.

As will be appreciated, adaptors may also comprise other elements,including recognition sites for other (non-Type IIs) restrictionendonucleases, primer binding sites for amplification as well as bindingsites for probes used in sequencing reactions (“anchor probes”),described further herein.

In one aspect, adaptors of use in the invention have sequences as shownin FIG. 5. As identified in the schematic of one of the adaptors in FIG.5B, adaptors can comprise multiple functional features, includingrecognition sites for Type IIs restriction endonucleases (503 and 506),sites for nicking endonucleases (504) as well as sequences that caninfluence secondary characteristics, such as bases to disrupt hairpins(501 and 502). Adaptors of use in the invention may in addition containpalindromic sequences, which can serve to promote intramolecular bindingonce nucleic acid templates comprising such adaptors are used togenerate concatemers, as is discussed in more detail below.

IV. Preparing Nucleic Acid Templates of the Invention

IVA. Overview of Generation of Circular Templates

The present invention is directed to compositions and methods fornucleic acid identification and detection, which finds use in a widevariety of applications as described herein, including a variety ofsequencing and genotyping applications. The methods described hereinallow the construction of circular nucleic acid templates that are usedin amplification reactions that utilize such circular templates tocreate concatamers of the monomeric circular templates, forming “DNAnanoballs”, described below, which find use in a variety of sequencingand genotyping applications. The circular or linear constructs of theinvention comprise target nucleic acid sequences, generally fragments ofgenomic DNA (although as described herein, other templates such as cDNAcan be used), with interspersed exogeneous nucleic acid adaptors. Thepresent invention provides methods for producing nucleic acid templateconstructs in which each subsequent adaptor is added at a definedposition and also optionally in a defined orientation in relation to oneor more previously inserted adaptors. These nucleic acid templateconstructs are generally circular nucleic acids (although in certainembodiments the constructs can be linear) that include target nucleicacids with multiple interspersed adaptors. These adaptors, as describedbelow, are exogenous sequences used in the sequencing and genotypingapplications, and usually contain a restriction endonuclease site,particularly for enzymes such as Type IIs enzymes that cut outside oftheir recognition site. For ease of analysis, the reactions of theinvention preferably utilize embodiments where the adaptors are insertedin particular orientations, rather than randomly. Thus the inventionprovides methods for making nucleic acid constructs that containmultiple adaptors in particular orientations and with defined spacingbetween them.

Control over the spacing and orientation of insertion of each subsequentadaptor provides a number of advantages over random insertion ofinterspersed adaptors. In particular, the methods described hereinimprove the efficiency of the adaptor insertion process, thus reducingthe need to introduce amplification steps as each subsequent adaptor isinserted. In addition, controlling the spacing and orientation of eachadded adaptor ensures that the restriction endonuclease recognitionsites that are generally included in each adaptor are positioned toallow subsequent cleavage and ligation steps to occur at the properpoint in the nucleic acid construct, thus further increasing efficiencyof the process by reducing or eliminating the formation of nucleic acidtemplates that have adaptors in the improper location or orientation. Inaddition, control over location and orientation of each subsequentlyadded adaptor can be beneficial to certain uses of the resultant nucleicacid construct, because the adaptors serve a variety of functions insequencing applications, including serving as a reference point of knownsequence to aid in identifying the relative spatial location of basesidentified at certain positions within the target nucleic acid. Suchuses of adaptors in sequencing applications are described furtherherein.

Genomic nucleic acid, generally double stranded DNA (601 in FIG. 6), isobtained from a plurality of cells, generally from about 10 to 100 to1000 to more cells. The use of a plurality of cells allows the ultimateDNA nanoballs to have a level of redundancy which allows for goodsequencing coverage of the genome. The genomic nucleic acid isfractionated into appropriate sizes using standard techniques such asphysical or enzymatic fractionation combined with size fractionation asis described herein.

The 5′ and 3′ ends of the double stranded fragments can optionally beadjusted, as described herein. For example, many techniques used tofractionate nucleic acids result in a combination of lengths andchemistries on the termini of the fragments. For example, the terminimay contain overlaps, and for many purposes, blunt ends of the doublestranded fragments are preferred. This can be done using knowntechniques such as a polymerase and dNTPs. Similarly, the fractionationtechniques may also result in a variety of termini, such as 3′ and 5′hydroxyl groups and/or 3′ and 5′ phosphate groups. In some embodiments,as described below, it is desirable to enzymatically alter thesetermini. For example, to prevent the ligation of multiple fragmentswithout the adaptors, it can be desirable to alter the chemistry of thetermini such that the correct orientation of phosphate and hydroxylgroups is not present, thus preventing “polymerization” of the targetsequences. The control over the chemistry of the termini can be providedusing methods known in the art. For example, in some circumstances, theuse of phosphatase eliminates all the phosphate groups, such that allends contain hydroxyl groups. Each end can then be selectively alteredto allow ligation between the desired components.

In addition, as needed, amplification can also optionally be conductedusing a wide variety of known techniques to increase the number ofgenomic fragments for further manipulation, although in manyembodiments, an amplification step is not needed at this step.

After fractionation and optional termini adjustment, a set of adaptor“arms” are added to the termini of the genomic fragments. The twoadaptor arms, when ligated together, form the first adaptor. Forexample, as depicted in FIG. 6, circularization (605) of a linearconstruct with an adaptor arm on each end of the construct ligates thetwo arms together to form the full adaptor (606) as well as the circularconstruct (607). Thus, a first adaptor arm (603) of a first adaptor isadded to one terminus of the genomic fragment, and a second adaptor arm(604) of a first adaptor is added to the other terminus of the genomicfragment. Generally, and as more fully described below, either or bothof the adaptor arms will include a recognition site for a Type IIsendonuclease, depending on the desired system. Alternatively, theadaptor arms can each contain a partial recognition site that isreconstituted upon ligation of the arms.

In order to ligate subsequent adaptors in a desired position andorientation for sequencing, the present invention provides a method inwhich a Type IIs restriction endonuclease binds to a recognition sitewithin the first adaptor of a circular nucleic acid construct and thencleaves at a point outside the first adaptor and in the genomic fragment(also referred to herein as the “target nucleic acid”). A second adaptorcan then be ligated into the point at which cleavage occurs (again,usually by adding two adaptor arms of the second adaptor). In order tocleave the target nucleic acid at a known point, it can be desirable toblock any other recognition sites for that same enzyme that may randomlybe encompassed in the target nucleic acid, such that the only point atwhich that restriction endonuclease can bind is within the firstadaptor, thus avoiding undesired cleavage of the constructs. Generally,the recognition site in the first adaptor is first protected frominactivation, and then any other unprotected recognition sites in theconstruct are inactivated, generally through methylation. That is,methylated recognition sites will not bind the enzyme, and thus nocleavage will occur. Only the unmethylated recognition site within theadaptor will allow binding of the enzyme with subsequent cleaving.

One method of protecting the recognition site in the first adaptor frominactivation is to make the site single stranded, as the methylationenzyme will not bind to a single strand. Thus, one method of protectingthe recognition site of the first adaptor is by amplifying the lineargenomic fragments ligated to the two first adaptor arms using primersmodified with uracil. The primers are complementary to the adaptor armsand are modified with uracil such that, upon amplification (generallyusing PCR), the resultant linear constructs contain uracil embedded inthe recognition site of one of the first adaptor arms. Digestion of theuracil using known techniques renders that first adaptor arm (orwhatever contains the uracil) single stranded. A sequence specificmethylase is then applied to the linear constructs that will methylateall of the double-stranded recognition sites for the same endonucleaseas that contained in the first adaptor. Such a sequence-specificmethylase will not be able to methylate the single stranded recognitionsite in the first adaptor arm, and thus the recognition site in thefirst adaptor arm will be protected from inactivation by methylation. Asdescribed below, if a restriction site is methylated, it will not becleaved by the restriction endonuclease enzyme.

In some cases, as more fully described below, a single adaptor may havetwo of the same recognition sites, to allow cleavage both “upstream” and“downstream” from the same adaptor. In this embodiment, as depicted inFIG. 7, the primers and uracil positions are chosen appropriately, suchthat either the “upstream” or “downstream” recognition site may beselectively protected from inactivation or inactivated. For example, inFIG. 7, the two different adaptor arms (represented as rectangles) eachcomprise a recognition site for a restriction endonuclease (representedby the circle in one adaptor arm and by a triangle in the other). If theadaptor arm with the recognition site represented by the circle needs tobe protected using the above-described uracil degradation method, thenthe uracil-modified amplification primers are designed to incorporateuracils into that recognition site. Then upon uracil degradation, thatadaptor arm is rendered single stranded (represented by thehalf-rectangles), thus protecting that recognition site frominactivation.

After protecting the recognition site in the first adaptor arm frommethylation, the linear construct is circularized, for example, by usinga bridge oligonucleotide and T4 ligase. The circularizationreconstitutes the double stranded restriction endonuclease recognitionsite in the first adaptor arm. In some embodiments, the bridgeoligonucleotide has a blocked end, which results in the bridgingoligonucleotide serving to allow circularization, ligating thenon-blocked end, and leaving a nick near the recognition site. This nickcan be further exploited as discussed below. Application of therestriction endonuclease produces a second linear construct thatcomprises the first adaptor in the interior of the target nucleic acidand termini comprising (depending on the enzyme) a two base overhang.

A second set of adaptor arms for a second adaptor is ligated to thesecond linear construct. In some cases, when a nick is utilized, inorder to ensure that the adaptors are ligated in the proper orientation,the nick in the first adaptor is “translated” (or “translocated”) byusing a polymerase with exonuclease activity. The exonuclease activityof the polymerase (such as Taq polymerase) will excise the short DNAstrand that abuts the nick while the polymerase activity will “fill in”the nick and subsequent nucleotides in that strand (essentially, the Taqmoves along the strand, excising bases using the exonuclease activityand adding the same bases, with the result being that the nick istranslocated along the strand until the enzyme reaches the end).

In addition, to create an asymmetry of the template, one termini of theconstruct is modified with a single base. For example, certainpolymerases, such as Taq, will undergo untemplated nucleotide additionto result in addition of a single nucleotide to the 3′ end of the bluntDNA duplex, resulting in a 3′ overhang. As will be appreciated by thosein the art, any base can be added, depending on the dNTP concentrationin the solution. In certain embodiments, the polymerase utilized willonly be able to add a single nucleotide. For example, Taq polymerasewill be able to add a single G or A. Other polymerases may also be usedto add other nucleotides to produce the overhang. In one embodiment, anexcess of dGTP is used, resulting in the untemplated addition of aguanosine at the 3′ end of one of the strands. This “G-tail” on the 3′end of the second linear construct results in an asymmetry of thetermini, and thus will ligate to a second adaptor arm, which will have aC-tail that will allow the second adaptor arm to anneal to the 3′ end ofthe second linear construct. The adaptor arm meant to ligate to the 5′end will have a C-tail positioned such that it will ligate to the 5′G-tail. After ligation of the second adaptor arms, the construct iscircularized to produce a second circular construct comprising twoadaptors. The second adaptor will generally contain a recognition sitefor a Type IIs endonuclease, and this recognition site may be the sameor different than the recognition site contained in the first adaptor,with the latter finding use in a variety of applications

A third adaptor can be inserted on the other side of the first adaptorby cutting with a restriction endonuclease bound to a recognition sitein the second arm of the first adaptor (the recognition site that wasoriginally inactivated by methylation). In order to make thisrecognition site available, uracil-modified primers complementary to thesecond recognition site in the first adaptor are used to amplify thecircular constructs to produce third linear constructs in which thefirst adaptor comprises uracils embedded in the second restrictionrecognition site. The uracils are degraded to render the first adaptorsingle stranded, which protects the recognition site in the adaptor frommethylation. Applying a sequence-specific methylase will then inactivateall unprotected recognition sites. Upon circularization the recognitionsite in the first adaptor is reconstituted, and applying the restrictionendonuclease will cleave the circle, producing a position at which thethird adaptor can be inserted in a third linear construct. Ligatingthird adaptor arms to the third linear construct will follow the samegeneral procedure described above—the third linear construct will be A-or G-tailed, the third adaptor arms will be T- or C-tailed, allowing theadaptor arms to anneal to the third linear construct and be ligated. Thelinear construct comprising the third adaptor arms is then circularizedto form a third circular construct. Like the second adaptor, the thirdadaptor will generally comprise a recognition site for a restrictionendonuclease that is different than the recognition site contained inthe first adaptor.

A fourth adaptor can be added by utilizing Type IIs restrictionendonucleases that have recognition sites in the second and thirdadaptors. Cleavage with these restriction endonucleases will result in afourth linear construct that can then be ligated to fourth adaptor arms.Circularization of the fourth linear construct ligated to the fourthadaptor arms will produce the nucleic acid template constructs of theinvention. As will be appreciated by those in the art, other adaptorscan be added. Thus, the methods described herein allow two or moreadaptors to be added in an orientation and sometimes distance dependentmanner.

The present invention also provides methods for controlling theorientation in which each subsequently added adaptor is inserted. Such“nick translation” methods provide a way to control the way targetnucleic acids and adaptors ligate to each other. These methods alsoprevent artifacts in the nucleic acid constructs by preventing ligationof adaptors to other adaptors and target nucleic acid molecules to othertarget nucleic acid molecules (essentially avoiding the “polymerization”of adaptors and target nucleic acid molecules). Examples of differentorientations in which adaptors and target nucleic acid molecules can beligated are schematically illustrated in FIG. 8. Target nucleic acids801 and 802 are preferably ligated to adaptors 803 and 804 in a desiredorientation (as illustrated in this figure, the desired orientation isone in which the ends with the same shape—circle or square—ligates toeach other). Modifying the ends of the molecules avoids the undesiredconfigurations 807, 808, 809 and 810, in which the target nucleic acidsligate to each other and the adaptors ligate to each other. In addition,as will be discussed in further detail below, the orientation of eachadaptor-target nucleic acid ligation can also be controlled throughcontrol of the chemistry of the termini of both the adaptors and thetarget nucleic acids. The control over the chemistry of the termini canbe provided using methods known in the art. For example, in somecircumstances, the use of phosphatase eliminates all the phosphategroups, such that all ends contain hydroxyl groups. Each end can then beselectively altered to allow ligation between the desired components.These and other methods for modifying ends and controlling insertion ofadaptors in the nick translation methods of the invention are describedin further detail below.

These nucleic acid template constructs (“monomers” comprising targetsequences interspersed with these adaptors) can then be used in thegeneration of concatemers, which in turn form the nucleic acid nanoballsthat can be used in downstream applications, such as sequencing anddetection of specific target sequences.

The present invention provides methods for forming nucleic acid templateconstructs comprising multiple interspersed adaptors inserted into atarget nucleic acid. As discussed further herein, methods of theinvention allow insertion of each subsequent adaptor by utilizingrecognition sites for Type IIs restriction endonucleases that areincluded in the adaptors. In order to insert multiple adaptors in adesired order and/or orientation, it can be necessary to blockrestriction endonuclease recognition sites contained within the targetnucleic acids, such that only the recognition site in the adaptor isavailable for binding the enzyme and the subsequent cleavage. Among theadvantages of such methods is that the same restriction endonucleasesite can be used in each adaptor, which simplifies production ofcircular templates that will eventually be used to generate concatemers,adaptors can be inserted using a previously inserted adaptor as a“stepping stone” for the next, such that addition can occur in effect by“walking” down the length of the fragment with each new adaptor.Controlling the recognition sites available for restriction enzymes alsoavoids the excision of certain sequences, thereby obtaining only limitedsequence representation (which could result if sites within the targetnucleic acid were accessible).

IVB. Adding a First Adaptor

As a first step in the creation of nucleic acid templates of theinvention, a first adaptor is ligated to a target nucleic acid. Theentire first adaptor may be added to one terminus, or two portions ofthe first adaptor, referred to herein as “adaptor arms”, can be ligatedto each terminus of the target nucleic acid. The first adaptor arms aredesigned such that upon ligation they reconstitute the entire firstadaptor. As described further above, the first adaptor will generallycomprise one or more recognition sites for a Type IIs restrictionendonuclease. In some embodiments, a Type IIs restriction endonucleaserecognition site will be split between the two adaptor arms, such thatthe site is only available for binding to a restriction endonucleaseupon ligation of the two adaptor arms.

FIG. 6 is a schematic representation of one aspect of a method forassembling adaptor/target nucleic acid templates (also referred toherein as “target library constructs”, “library constructs” and allgrammatical equivalents). DNA, such as genomic DNA 601, is isolated andfragmented into target nucleic acids 602 using standard techniques asdescribed above. The fragmented target nucleic acids 602 are thenrepaired so that the 5′ and 3′ ends of each strand are flush or bluntended. Following this reaction, each fragment is “A-tailed” with asingle A added to the 3′ end of each strand of the fragmented targetnucleic acids using a non-proofreading polymerase. The A-tailing isgenerally accomplished by using a polymerase (such as Taq polymerase)and providing only adenosine nucleotides, such that the polymerase isforced to add one or more A's to the end of the target nucleic acid in atemplate-sequence-independent manner.

In the exemplary method illustrated in FIG. 6, a first (603) and secondarm (603) of a first adaptor is then ligated to each target nucleicacid, producing a target nucleic acid with adaptor arms ligated to eachend. In one embodiment, the adaptor arms are “T tailed” to becomplementary to the A tails of the target nucleic acid, facilitatingligation of the adaptor arms to the target nucleic acid by providing away for the adaptor arms to first anneal to the target nucleic acids andthen applying a ligase to join the adaptor arms to the target nucleicacid.

In a further embodiment, the invention provides adaptor ligation to eachfragment in a manner that minimizes the creation of intra- orintermolecular ligation artifacts. This is desirable because randomfragments of target nucleic acids forming ligation artifacts with oneanother create false proximal genomic relationships between targetnucleic acid fragments, complicating the sequence alignment process.Using both A tailing and T tailing to attach the adaptor to the DNAfragments prevents random intra- or inter-molecular associations ofadaptors and fragments, which reduces artifacts that would be createdfrom self-ligation, adaptor-adaptor or fragment-fragment ligation.

As an alternative to NT tailing (or G/C tailing), various other methodscan be implemented to prevent formation of ligation artifacts of thetarget nucleic acids and the adaptors, as well as orient the adaptorarms with respect to the target nucleic acids, including usingcomplementary NN overhangs in the target nucleic acids and the adaptorarms, or employing blunt end ligation with an appropriate target nucleicacid to adaptor ratio to optimize single fragment nucleic acid/adaptorarm ligation ratios.

After creating a linear construct comprising a target nucleic acid andwith an adaptor arm on each terminus, the linear target nucleic acid iscircularized (605), a process that will be discussed in further detailherein, resulting in a circular construct 607 comprising target nucleicacid and an adaptor. Note that the circularization process results inbringing the first and second arms of the first adaptor together to forma contiguous first adaptor (606) in the circular construct. In someembodiments, the circular construct 607 is amplified, such as by circledependent amplification, using, e.g., random hexamers and φ29 orhelicase. Alternatively, target nucleic acid/adaptor structure mayremain linear, and amplification may be accomplished by PCR primed fromsites in the adaptor arms. The amplification preferably is a controlledamplification process and uses a high fidelity, proof-readingpolymerase, resulting in a sequence-accurate library of amplified targetnucleic acid/adaptor constructs where there is sufficient representationof the genome or one or more portions of the genome being queried.

IVC. Adding Multiple Adaptors

FIG. 6 is a schematic representation of one aspect of a method forassembling adaptor/target nucleic acid templates (also referred toherein as “target library constructs”, “library constructs” and allgrammatical equivalents). DNA, such as genomic DNA 601, is isolated andfragmented into target nucleic acids 102 using standard techniques. Thefragmented target nucleic acids 602 are then in some embodiments (asdescribed herein) repaired so that the 5′ and 3′ ends of each strand areflush or blunt ended.

In the exemplary method illustrated in FIG. 6, a first (603) and secondarm (604) of a first adaptor is ligated to each target nucleic acid,producing a target nucleic acid with adaptor arms ligated to each end.

After creating a linear construct comprising a target nucleic acid andwith an adaptor arm on each terminus, the linear target nucleic acid iscircularized (605), a process that will be discussed in further detailherein, resulting in a circular construct 607 comprising target nucleicacid and an adaptor. Note that the circularization process results inbringing the first and second arms of the first adaptor together to forma contiguous first adaptor (606) in the circular construct. In someembodiments, the circular construct 607 is amplified, such as by circledependent amplification, using, e.g., random hexamers and φ29 orhelicase. Alternatively, target nucleic acid/adaptor structure mayremain linear, and amplification may be accomplished by PCR primed fromsites in the adaptor arms. The amplification preferably is a controlledamplification process and uses a high fidelity, proof-readingpolymerase, resulting in a sequence-accurate library of amplified targetnucleic acid/adaptor constructs where there is sufficient representationof the genome or one or more portions of the genome being queried.

Similar to the process for adding the first adaptor, a second set ofadaptor arms (610) and (611) can be added to each end of the linearmolecule (606) and then ligated (612) to form the full adaptor (614) andcircular molecule (613). Again, a third adaptor can be added to theother side of adaptor (606) by utilizing a Type IIs endonuclease thatcleaves on the other side of adaptor (606) and then ligating a third setof adaptor arms (617) and (618) to each terminus of the linearizedmolecule. Finally, a fourth adaptor can be added by again cleaving thecircular construct and adding a fourth set of adaptor arms to thelinearized construct. The embodiment pictured in FIG. 6 is a method inwhich Type IIs endonucleases with recognition sites in adaptors (620)and (614) are applied to cleave the circular construct. The recognitionsites in adaptors (620) and (614) may be identical or different.Similarly, the recognition sites in all of the adaptors illustrated inFIG. 6 may be identical or different.

As generally illustrated in FIG. 9, a circular construct comprising afirst adaptor may contain two Type IIs restriction endonucleaserecognition sites in that adaptor, positioned such that the targetnucleic acid outside the recognition sequence (and outside of theadaptor) is cut (910). The arrows around structure 510 indicate therecognition sites and the site of restriction. In process 911, EcoP15, aType IIs restriction endonuclease, is used to cut the circularconstruct. Note that in the aspect shown in FIG. 9, a portion of eachlibrary construct mapping to a portion of the target nucleic acid willbe cut away from the construct (the portion of the target nucleic acidbetween the arrow heads in structure 910). Restriction of the libraryconstructs with EcoP15 in process 911 results in a library of linearconstructs containing the first adaptor, with the first adaptor“interior” to the ends of the linear construct 912. The resulting linearlibrary construct will have a size defined by the distance between theendonuclease recognition sites and the endonuclease restriction siteplus the size of the adaptor. In process 913, the linear construct 912,like the fragmented target nucleic acid 904, is treated by conventionalmethods to become blunt or flush ended, A tails comprising a single Aare added to the 3′ ends of the linear library construct using anon-proofreading polymerase and first and second arms of a secondadaptor are ligated to ends of the linearized library construct by A-Ttailing and ligation 913. The resulting library construct comprises thestructure seen at 914, with the first adaptor interior to the ends ofthe linear construct, with target nucleic acid flanked on one end by thefirst adaptor, and on the other end by either the first or second arm ofthe second adaptor.

In process 915, the double-stranded linear library constructs aretreated so as to become single-stranded 916, and the single-strandedlibrary constructs 916 are then ligated 917 to form single-strandedcircles of target nucleic acid interspersed with two adaptors 918. Theligation/circularization process of 917 is performed under conditionsthat optimize intramolecular ligation. At certain concentrations andreaction conditions, the local intramolecular ligation of the ends ofeach nucleic acid construct is favored over ligation between molecules.

IVD. Controlling Orientation of Ligation Between Target Nucleic Acidsand Adaptors

In one aspect, the present invention provides methods in which ligationof adaptors to target nucleic acids, as described above, is accomplishedin a desired orientation. Such control over orientation is advantageous,because random fragments of target nucleic acids forming ligationartifacts with one another create false proximal genomic relationshipsbetween target nucleic acid fragments, complicating the sequencealignment process.

There are several methods that find use in controlling orientation ofthe adaptor insertion. As described above, altering the chemistry of thetermini of the targets and the adaptors can be done, such that ligationcan only occur when the correct orientation is present. Alternatively,“nick translation methods” can be done, which also rely on the terminichemistries, as outlined below. Finally, methods involving amplificationwith specific choices of primers can be done as described below.

FIG. 12 is a schematic illustration of the different orientations inwhich a second adaptor may be added to a nucleic acid construct. Again,process 1200 begins with circular library construct 1202, having aninserted first adaptor 1210. First adaptor 1210 has a specificorientation, with a rectangle identifying the “outer strand” of thefirst adaptor and a diamond identifying the “inner strand” of the firstadaptor (Ad1 orientation 1210). A Type IIs restriction endonuclease sitein the first adaptor 1210 is indicated by the tail of arrow 1201, andthe site of cutting is indicated by the arrow head. Process 1203comprises cutting with the Type IIs restriction endonuclease, ligatingfirst and second adaptor arms of a second adaptor, andrecircularization. As can be seen in the resulting library constructs1204 and 1206, the second adaptor can be inserted in two different waysrelative to the first adaptor. In the desired orientation 1204, the ovalis inserted into the outer strand with the rectangle, and the bowtie isinserted into the inner strand with the diamond (Ad2 orientation 1220).In the undesired orientation the oval is inserted into the inner strandwith the diamond and the bowtie is inserted into the outer strand withthe rectangle (Ad2 orientation 1230).

Although much of the following discussion and referenced illustrativefigures discuss for clarity's sake insertion of a second adaptor inrelation to a first, it will be appreciated that the processes discussedherein are applicable to adaptors added subsequently to the secondadaptor, creating library constructs with three, four, five, six, seven,eight, nine, ten or more inserted adaptors.

In one embodiment, both A tailing and T tailing are used to attach anadaptor to a nucleic acid fragment. For example, following themodifications described above to repair the ends of fragments, eachfragment can be “A-tailed” with a single A added to the 3′ end of eachstrand of the fragmented target nucleic acids using a non-proofreadingpolymerase. The A-tailing is generally accomplished by using apolymerase (such as Taq polymerase) and providing either only adenosinenucleotides (or an excess thereof), such that the polymerase is forcedto add one or more A's to the end of the target nucleic acid in atemplate-sequence-independent manner. In embodiments in which“A-tailing” is used, ligation to adaptor (or adaptor arms) can beaccomplished by adding a “T-tail” to the 5′ end of the adaptor/adaptorarms to be complementary to the A tails of the target nucleic acid,facilitating ligation of the adaptor arms to the target nucleic acid byproviding a way for the adaptor arms to first anneal to the targetnucleic acids and then applying a ligase to join the adaptor arms to thetarget nucleic acid.

Because the aspects of the claimed invention work optimally when nucleicacid templates are of a desired size and comprise target nucleic acidderived from a single fragment, it can be beneficial to ensure thatthroughout the process of producing nucleic acid templates that thecircularization reactions occur intramolecularly. That is, it can bebeneficial to ensure that target nucleic acids in the process of beingligated to a first, second, third, etc. adaptor do not ligate to oneanother. One embodiment of controlling the circularization process isillustrated in FIG. 10. As shown in FIG. 10, blocking oligos 1017 and1027 are used to block the binding regions 1012 and 1022 regions,respectively. Blocker oligonucleotide 1017 is complementary to bindingsequence 1016, and blocker oligonucleotide 1027 is complementary tobinding sequence 1026. In the schematic illustrations of the 5′ adaptorarm and the 3′ adaptor arm, the underlined bases are dideoxycytosine(ddC) and the bolded font bases are phosphorylated. Blockeroligonucleotides 1017 and 1027 are not covalently bound to the adaptorarms, and can be “melted off” after ligation of the adaptor arms to thelibrary construct and before circularization; further, the dideoxynucleotide (here, ddC or alternatively a different non-ligatablenucleotide) prevents ligation of blocker to adaptor. In addition or asan alternative, in some aspects, the blocker oligo-adaptor arm hybridscontain a one or more base gap between the adaptor arm and the blockerto reduce ligation of blocker to adaptor. In some aspects, theblocker/binding region hybrids have T_(m)s of about 37° C. to enableeasy melting of the blocker sequences prior ligation of the adaptor arms(circularization).

IVD(i). Controlling Orientation of Ligation: Arm-by-Arm Ligation

In one aspect, the directional insertion of adaptors can be controlledwithout modifying the termini of the target nucleic acid using an“arm-by-arm” ligation method. In general, this is a two-step ligationprocess in which an adaptor arm is added to a target nucleic acid andprimer extension with strand displacement produces two double strandedmolecules each with an adaptor arm on one end—a second adaptor arm canthen be ligated to the terminus without an adaptor arm. This process canprevent the creation of nucleic acid molecules that comprise the sameadaptor arm on both termini—for example, as depicted in FIG. 11A, thearm-by-arm ligation process can prevent the formation of nucleic acidmolecules that have both termini occupied by Adaptor A or Adaptor B. Inmany embodiments it is preferred that each terminus of a target nucleicacid is ligated to a different adaptor arm, such that when the two armsare ligated they are able to form a complete whole adaptor. This can beparticularly useful for minimizing the number of amplification stepsthat are needed after addition of each adaptor arm, because thearm-by-arm ligation reduces the number of non-useful molecules producedin each ligation reaction.

FIG. 11 illustrates one embodiment of the arm-by-arm ligation method. Inthis embodiment, one strand of the first adaptor arm A is added to bothstrands of a dephosphorylated target nucleic acid. This adaptor arm isblocked on one end (depicted as the closed circle), generally by usingalkaline phosphatase. Primer exchange can be used to replace the strandwith the blocked end. Primer extension with strand displacement (whichcan be accomplished, in one exemplary embodiment, through the use ofphi29 or Pfu polymerase) will prime from both ends and extend throughthe whole insert, resulting in two double-stranded nucleic acidmolecules, each with an adaptor arm A on one terminus and a blunt end onthe other. In an alternative embodiment, adaptor arm A can be usedpre-hybridized with a primer upstream of the blocked strand to initiateprimer extension without requiring a primer exchange reaction. After thestrand-displacing polymerase reaction, a second adaptor arm B can thenbe ligated, generally to the blunt end of the target nucleic acid ratherthan to the terminus with the adaptor arm. This arm-by-arm ligationprocess can prevent the formation of target nucleic acids that comprisethe same adaptor arm on both termini.

IVD(ii). Controlling Orientation of Ligation: Nick Translation Methods

In one embodiment, the present invention provides “nick translationmethods” for constructing nucleic acid molecules. In one embodiment,nick translation methods are used to ligate nucleic acid molecules in adesired orientation. In a further embodiment, nick translation methodsare used for inserting adaptors in a desired orientation. Such methodsgenerally involve modifying one or both termini of one or both of thenucleic acid molecules to be ligated together. For example, whenligating an adaptor to a target nucleic acid, one or both termini ofeither or both the target nucleic acid and adaptor to be ligated aremodified. Following such modification, a “translocation” or“translation” of a nick inserted into one strand of a construct providesthe ability to control the final orientation of the ligatedadaptor-target nucleic acid construct. “Nick translation methods” asdescribed herein may also include primer extension or gap-fill-inmethods, as is described in further detail below. Although the followingdiscussion is provided in terms of controlling ligation of adaptors totarget nucleic acids, it will be appreciated that these methods are notlimited to ligation of adaptors and target nucleic acids, and that thesemethods can also be used to control ligation of any two nucleic acidmolecules. For example, nick translation methods and any othercontrolled ligation methods described herein can be used as part ofgenetic and/or DNA engineering methods, such as the construction of newplasmids or other DNA vectors, gene or genome synthesis ormodifications, as well as in constructing building blocks fornanotechnology constructs.

FIG. 13 is a schematic illustration of such a “nick translation” type ofprocess. Construct 1306 in FIG. 13 is formed using methods discussedherein, and has an interspersed adaptor 1304, with a restrictionendonuclease recognition site (tail of the arrow in FIG. 13), and acleavage site. In FIG. 14, the library construct is not circularized,but is a branched concatemer of alternating target nucleic acidfragments 1406 (with restriction endonuclease recognition sites 1404)and adaptors 1412; however, the nick translation type process shown inFIG. 13 may be performed on such a library construct configuration aswell. The term “library construct” as used herein refers to nucleic acidconstructs comprising one or more adaptors, and is interchangeable withthe term “nucleic acid template”.

The library constructs with an inserted first adaptor are digested by arestriction endonuclease (process 1301)—in certain aspects, a Type IIsrestriction endonuclease—that cuts the target nucleic acid to render 3′nucleotide overhangs 1308. In FIG. 11, two nucleotides (NN-3′) 1308 areshown, though the number of overhanging nucleotides varies inalternative aspects depending at least in part on the identify of therestriction endonuclease used. The library construct 1310 is linearized,with the first inserted adaptor shown at 1304. The first insertedadaptor 1304 is engineered such that it comprises either a nick 1312 atthe boundary of the adaptor fragment or it comprises the recognitionsite for a nicking endonuclease that permits the introduction of a nick1314 at the interior of the adaptor. In either case, library construct1310 is treated 1303 with a polymerase 1316 that can extend the upperstrand from nick 1312 or 1314 to the end of the lower strand of libraryconstruct 1310 to form a strand having a 3′ overhang at one end and ablunt end at the other. To this library construct 1310, a second adaptor1318 is ligated in process 1305, where the second adaptor 1318 has adegenerate nucleotide overhang at one end and a single 3′ nucleotide(e.g., dT) overhang at the other end to form library construct 1320.Library construct 1320 is then treated (e.g., with Taq polymerase) inprocess 1307 to add a 3′ dA to the blunt end. Library construct 1322 maythen be amplified by PCR, with, e.g., uracil-containing primers.Alternatively, library construct 1322 may then be circularized inprocess 1309 in which case CDA may be performed (such as in step 1421 ofFIG. 14). Combining the processes discussed herein with the nicktranslation type process shown in FIG. 13 allows for selecting both therelative position and relative orientation of subsequently-addedadaptors to any adaptors previously inserted into the libraryconstructs.

In order to utilize a nick translation type of procedure, it may bebeneficial to modify one or both of the termini of the target nucleicacid and/or the adaptor as discussed above. In one exemplary embodiment,a first arm of an adaptor that is meant to ligate to the 3′ end of atarget nucleic acid may be designed such that its 3′ terminus isblocked, such that only the 5′ end of the adaptor arm is available toligate to only the 3′ end of the target nucleic acid. Similarly, thesecond arm that is meant to ligate to the 5′ end of the target nucleicacid may be designed such that its 5′ end is blocked, such that only the3′ end of the second arm can ligate to the 5′ end of the target nucleicacid. Methods for blocking one terminus of the adaptor arm and/or thetarget nucleic acid are well known in the art. For example, the targetnucleic acid (which is also referred to herein as a “nucleic acidinsert” or a “DNA insert” or an “insert”) is treated with enzymes thatgenerate defined functional ends and remove phosphates from both the 3′and 5′ ends as discussed above. Removing all of the phosphate groupsrenders the target nucleic acid molecules unable to ligate to eachother. Adaptors in this embodiment are also designed to have one strandcapable of ligation (for example by creating or maintaining a 5′phosphate group) and a complementary strand that has a 3′ end that isprotected from ligation. Generally, this protection of the 3′ end isaccomplished using a dideoxy nucleotide to inactivate the 3′ end. Thus,when the modified target nucleic acids lacking phosphate groups on bothends and modified adaptors comprising only a phosphate group on one 5′end with a 3′ block (for example, a dideoxy) on the complementarystrand, the only ligation product that will form is that of targetnucleic acid ligated to the 5′ end of the adaptor that has a phosphategroup. Subsequent to this ligation step, the protected 3′ end of theadaptor can be exchanged with a strand containing a functional 3′ end.This exchange is generally accomplished by taking advantage of the factthat the strand with 3′ protection is generally short and easy todenature. The exchange strand with a functional 3′ end is longer andwill thus bind more efficiently to the complementary strand—in furtherembodiments, the strand with the functional end is also added in higherconcentrations to further influence the reaction toward exchanging theprotected strand with the strand with the functional end. This strandwith the functional 3′ end is then primed by adding a DNA polymerasewith nick translation activity, such that the polymeraseexonucleolytically removes bases from the 5′ end of the target nucleicacid, thereby exposing a functional 5′ phosphate. This newly generated5′ phosphate can be ligated to the extension product by a ligase. (Ifligase is absent during the extension reaction, two polymerase moleculeswill nick translate from each end of the target nucleic acid until theymeet each other, resulting in a broken molecule). For example, asillustrated in FIG. 2, the target nucleic acid (insert) is firstend-repaired to form defined functional ends, preferentially blunt-ends.Next, to avoid concatemerization of inserts, 5′-end phosphates areremoved. The insert is then mixed with DNA ligase and DNA adaptors. TheDNA adaptor contains two oligonucleotides, and has one blunt-end and onesticky-end when the two oligonucleotides are hybridized together. Theblunt-end side contains one “top-strand” with a protected/inactivated3′-end, and one “bottom-strand” with a functional 5′-end phosphate, andare thus also unable to self-ligate. The only possible ligationcombination is therefore one insert with one “bottom-strand”blunt-ligated to each end. The “top-strand” with 3′-end protection isthen exchanged with an oligonucleotide containing a functional 3′-endthat can act as a primer in a polymerase extension reaction. Uponaddition of polymerase and ligase, the second oligonucleotide can bebuilt-in through a nick translation and ligation reaction. When thepolymerase is extending into the insert, it introduces a nick with afunctional 5′-end phosphate that can be recognized and sealed by DNAligase. The resulting insert with an adaptor or adaptor arm on each sideof each strand can now be subjected to PCR using primers specific to theadaptor.

Generally in a nick translation reaction such as the one describedabove, an active ligase is present or added in the mixture beforeaddition of the polymerase or simultaneously with the polymerase. Insome embodiments, it can be beneficial to use low activity polymerase(slow nick translation) conditions. Both addition of the ligase beforeor simultaneously with the polymerase and low activity conditions canhelp assure that the translating nick is sealed before reached theopposite end of the DNA fragment. In some embodiments, this can achievedby incubating the Taq polymerase with T4 ligase at 37° C., a temperaturethat will usually result in low polymerase activity and high ligaseactivity. The reaction may then be further incubated at a highertemperature (such as 50-60° C.) to further assurenick-translation-ligation occurs to completion across most/allconstructs in the reaction.

In further embodiments, the present invention provides methods forforming nucleic acid template constructs comprising multipleinterspersed adaptors. Methods of the present invention include methodsof inserting multiple adaptors such that each subsequent adaptor isinserted in a defined position with respect to one or more previouslyadded adaptors. Certain methods of inserting multiple interspersedadaptors are known in the art, for example, as discussed in U.S.Application Ser. Nos. 60/992,485; 61/026,337; 61/035,914; 61/061,134;61/116,193; 61/102,586; 12/265,593; 12/266,385; 11/679,124; 11/981,761;11/981,661; 11/981,605; 11/981,793 and 11/981,804, each of which isherein incorporated by reference in its entirety for all purposes and inparticular for all teachings related to methods and compositions forcreating nucleic acid templates comprising multiple interspersedadaptors as well as all methods for using such nucleic acid templates.Insertion of known adaptor sequences into target sequences, such thatthere is an interruption of contiguous target sequence with the multipleinterspersed adaptors, provides the ability to sequence both “upstream”and “downstream” of each adaptor, thus increasing the amount of sequenceinformation that can be generated from each nucleic acid template. Thepresent invention provides further methods for inserting each subsequentadaptor in a defined position with respect to one or more previouslyadded adaptors.

Nick translation ligation is usually performed after ligating the firststrand by adding at least polymerase to the reaction. In someembodiments, the nick translation reaction may be performed as aone-step reaction by adding all components at once, while in someembodiments the steps of the reaction are performed sequentially. Thereare multiple possible embodiments of a “one-step” approach of the nicktranslation reaction. For example, a single mix with a primer can beused in which Taq is added at the beginning of the reaction. Use of athermo-stable ligase provides the ability of performing primer exchangeand nick translation ligation (and PCR if necessary) by simplyincreasing the temperature. In another exemplary embodiment, thereaction mixture will contain a minimal concentration of non-processivenick-translating polymerase with a weak 3′ exonuclease that activatesthe 3′ blocked strand.

In a further embodiment, T4 polynucleotide kinase (PNK) or alkalinephosphatase is used to alter 3′ ends of adaptors and/or target nucleicacids to prepare them for a nick translation process. For example,adaptors can be inserted as part of a circularization reaction.End-repaired and alkaline phosphatase treated target nucleic acids areligated to adaptors, and in this exemplary embodiment are designed toform self-complementary hairpin shaped units (FIG. 16). The hairpins aredesigned to contain modifications at a given position that can berecognized and cleaved by enzymes or chemicals. For example, if thehairpins contain deoxyuridines, the deoxyuridiines can be recognized andcut by UDG/EndoVIII. After cutting, the two hairpins becomesingle-stranded with phosphates on their respective 3-end. These 3′phosphates can then be removed by either T4 Polynucleotide Kinase (PNK)or alkaline phosphatase (SAP) to enable nick-translation methods asdescribed further herein. In an exemplary embodiment such as the oneillustrated in FIG. 4A, the two hairpins are designed to be partlycomplementary to each other and can thus form, by intra-molecularhybridization, circularized molecules. Finally, the circularizedmolecules are subjected to a nick-translation process in which apolymerase extends into the insert and introduces a nick with afunctional 5′-end phosphate that can be recognized and sealed by DNAligase.

Instead of using hairpins as described above, a pair of double strandedadaptors that are partly complementary to each other can be used forcircularization. One pair has deoxyuridines on one strand that can berecognized and cut by UDG/EndoVIII. Other methods of nicking one strandcan also be used, including without limitation: nicking enzymes,incorporating inosine modified DNA that can be recognized byendonucleolytic enzymes, and incorporating DNA with RNA modificationsthat can be recognized by RNA-endonucleases. The target nucleic acid andadaptors can be prepared for controlled ligation as described above, forexample by treating the target nucleic acid with alkaline phosphatase tocreate blunt ends that are unable to ligate to other target nucleicacid. Circularization is activated by denaturing the short 3′-protectedstrand in the adaptor from the strand ligated to the target nucleicacid, leaving two partly complementary single stranded ends on each endof the target nucleic acid insert. The ends are then joined byintra-molecular hybridization and subjected to nick-translation andligation, forming a covalently closed circle. The circles are thentreated with UDG/EndoVIII to prepare the circle for directionalinsertion of the next adaptor.

In a still further embodiment illustrated in FIG. 15, a linear targetnucleic acid is treated with shrimp alkaline phosphatase (SAP) to remove5′ phosphates. Next, the target nucleic acid is ligated to one arm ofthe adaptor (arm A), containing a strand with a 5′ phosphate, and acomplementary shorter strand with a protected 3′ end. The ligationproduct is then subjected to nick-translation. The nick generated in thecircularization reaction is located on the top strand of the firstadaptor, and acts as a primer for the polymerase used in thenick-translation reaction. The polymerase extends the top-strand to thenick at the adaptor-insert junction, releasing one of the adaptor A armsand generating blunt end or A or G overhang. Next, the resultingpolymerase-generated insert end is ligated to the second adaptor arm(arm B). By designing the first adaptor to generate a nick in thecircularization reaction, the subsequent adaptor can be added in apredetermined orientation. This strategy is applicable for all type IIsrestriction enzymes or other enzymatic or non-enzymatic fragmentingmethods regardless of whether they generate a digested product that hasblunt ends, 3′ overhangs, or 5′ overhangs. The subsequent primerexchange, extension, ligation, and PCR is similar to that described inFIG. 2. A no-amplification option may also be used to close the circlecomprising melting off the blocked oligonucleotides followed by DNAcircularization via nick translation ligation reaction.

Both proofreading polymerases (which have 3′-5′ exonuclease activity),such as Pfu polymerase, and non-proofreading polymerases (which lack3′-5′ exonuclease activity), such as Taq polymerase, can be used in thenick translation and strand synthesis with strand displacement processesdescribed herein. Proofreading polymerases can efficiently generateblunt-ends in the nick translation process but have the disadvantage ofalso degrading non-protected 3′ overhangs. The resulting nicktranslation product will therefore have two blunt ends and will thus beunable to ligate subsequent adaptors in defined orientation. Onesolution is to protect the 3′ end of the ligated adaptor (arm A in FIG.15 for example) from degradation, using e.g. dideoxyribonucleosidetriphosphates (ddNTP) on the 3′ ends. However, ddNTP protection alsoprotects the 3′ end from subsequent extension, thus limiting theadaptors to be carried forward in a direct circularization procedure.Another potential solution is to protect the 3′ ends from polymerasedegradation using modifications on the 3′ end (e.g. 3′ phosphate) thatcan be removed prior to nick translation circularization (e.g. usingalkaline phosphatase). Another approach is to use hairpin shapedadaptors (as described in FIG. 16) in combination with proofreadingpolymerase in nick translation reactions. These adaptors will beprotected from degradation but have the disadvantage of requiring anextra UDG/EndoVIII step. Furthermore, the inventors have found that oneof the proofreading polymerases, Pfu polymerase, is able to efficientlygenerate blunt ends without degrading the non-protected 3′ overhang,indicating a low 3′-5′ exonuclease activity.

Non-proofreading polymerases, such as Taq polymerase, can generate bothblunt ends and single base overhangs in the nick translation process(Taq can generate non-templated A- and G-tails in addition to bluntends). An advantage of using polymerases without 3′-5′ exonucleaseactivity in the nick translation process is that non-protected 3′overhangs remain intact. This enables ligation of subsequent adaptors indefined orientation without protecting 3′ overhangs from degradation. Apotential disadvantage with many proofreading polymerases is that theyhave a function of adding single nucleotides on 3′ ends in anon-templated process. This process can be hard to control, and willoften generate a mixed population of 3′ ends, resulting in a lowadaptor-to-insert ligation yield. In general, methods utilizing bluntend ligation are more efficient than one base overhang ligation.

In one embodiment, after ligation of a first adaptor, rather thanforming a circle and then cleaving with a type IIs endonuclease that hasa recognition site in the first adaptor (which is a step in someembodiments of producing nucleic acid templates of the invention, suchas embodiments schematically illustrated in FIGS. 6 and 9), a secondadaptor can be added using a variation of the nick translation method.Exemplary embodiments of this variation are schematically illustrated inFIG. 17. In general, these embodiments begin with addition of a firstadaptor to a target nucleic acid and then circularization, as isdescribed in detail above and illustrated in FIGS. 6 and 9. In theembodiment illustrated in FIG. 17A, a nick translation is carried outusing a polymerase with 5′-3′ exonuclease activity (such as Taqpolymerase), which generates an inverted circle with the first adaptorlocated in the interior of the target nucleic acid. This product canthen be end-repaired and subjected to ligation to adaptor 2 (usingmethods described in further detail above). One disadvantage of thisembodiment is that the target nucleic acid may be longer than isrequired for sequencing application, and such longer templates might beprone to generating secondary structures in any nucleic acid concatemerproducts generated from the templates (the generation of concatemersfrom nucleic acid templates of the invention is discussed in greaterdetail below). Such secondary structures may result in a decreasedsignal when these concatemers are used in sequencing applications, suchas the cPAL methods discussed below. One way to overcome thisdisadvantage is by shortening the target nucleic acid—one exemplaryembodiment of this approach is pictured in FIG. 17B. In this embodiment,the first adaptor is modified with uracils using methods describedherein. Following the nick translation-inversion of the circlecomprising the first adaptor, an adaptor C-arm is added to both ends ofthe end-repaired molecule. The uracil-modified adaptor 1 is treated toremove the uracils, creating gaps, and also treated to generateactivated 3′ ends. Generally, the uracils are removed by application ofan UDG/EndoVIII enzyme mix and PNK and/or alkaline phosphatase is usedto remove the 3′ phosphates and generate activated 3′ ends. Theactivated 3′ ends of the adaptor 1 and the 3′ ends of adaptor arm C arerecognized by a nick translation polymerase (i.e., a polymerase with5′-3′ exonuclease activity) resulting in a product with adaptor 1surrounded by a target nucleic acid that has been trimmed toapproximately half of its original length. This polymerase cuttingprocedure can be repeated to decrease the size of the target nucleicacid even further if adaptor 1 is modified with additional nickingmodifications (including without limitation incorporation of inosine,RNA-modifications, and the like).

In a further embodiment, the nick translation methods illustrated inFIGS. 17A and B can be expanded to insert multiple adaptors. Bymodifying adaptors, nicks or gaps and functional 3′ ends can begenerated to prime nick translation reactions from multiple adaptorssimultaneously. A nucleic acid construct comprising target nucleic acidand two adaptors, each containing a uracil modification on one strand,is circularized. Next, the circle is treated with an enzyme mix, such asUDG/EndoVIII, to remove the uracils and introduce gaps. These gaps canbe simultaneously nick translated to invert the circle, making theconstruct available for ligation to additional adaptors. By addingmultiple modifications on the same adaptors, subsequent nicking/gappingand nick translation inversion can be carried out to introduce multipleadaptors. In some embodiments, uracils can be added back to the samepositions in the adaptors, making the adaptors suitable for further nicktranslation reactions. Adding the uracils back can be accomplished, forexample, by incubating the nick translation reaction with uracil only to“build back” the modification in the adaptor, followed by addition ofnon-modified nucleotides in higher concentration to fill in the rest ofthe construct.

In a still further embodiment, the target nucleic acid may be trimmed bycontrolling the speed of the nick translation enzyme. For example, thenick translation enzyme can be slowed by altering the temperature orlimiting reagents, which can result in two nicks being introduced intothe circularized insert that are shifted from the initial sites in theadaptor using a nick translation process. Similarly, using a stranddisplacement polymerase (such as phi29) will result in a nick beingshifted, producing a branching point due to a displaced segment of thenucleic acid. These nick or branch points can be recognized by variousenzymes (including without limitation S1 endonuclease, BaI31, T7endonculease, Mung Bean endonuclease, as well as combinations ofenzymes, such as a 5′ to 3′ exonuclease such as T7 exonuclease and S1 orMung Bean endonuclease) that will cut the opposite strand of the nick,resulting in a linear product. This product can then be end-repaired (ifneeded) and then ligated to the next adaptor. The size of the targetnucleic acid remaining will be controlled by the speed of the nicktranslation reaction, again for example by lowering the concentration ofreagents such as dNTPs or by conducting the reaction at a less thanoptimal temperature. The size of the target nucleic acid may also becontrolled by the incubation time of the nick translation reaction.

In a further embodiment, nick translation methods can be used to formnucleic acid templates without transitioning through any circularizingsteps. An exemplary embodiment of such methods is illustrated in FIG.18, which shows that the first adaptor 1801, which is shaped as ahairpin, is ligated to target nucleic acid 1802 using ligation methodsdescribed above, such as by treating the target nucleic acid with shrimpalkaline phosphate to remove phosphate groups and thereby control theends of the target nucleic acid that are available to ligate to thefirst adaptor. After ligation of the first adaptor, a controlleddouble-strand specific 5′-3′ exonuclease reaction is carried out togenerate single stranded 3′ ends. In some embodiments, the exonucleasereaction is carried out using a T7 exonuclease, although it will beappreciated that other double-strand specific exonucleases can be usedin this embodiment of the invention. In further embodiments, theexonuclease reaction generates single stranded 3′ ends of about 100 toabout 3000 bases in length. In still further embodiments, theexonuclease reaction generates single stranded 3′ ends of about 150 toabout 2500, about 200 to about 2000, about 250 to about 1500, about 300to about 1000, about 350 to about 900, about 400 to about 800, about 450to about 700, and about 500 to about 600 bases in length.

It will be appreciated that the nick translation processes describedherein can be used in combination with any of the other methods ofadding adaptors described herein. For example, the arm-by-arm ligationprocess described above and schematically illustrated in FIG. 11A can beused in combination with a nick translation process to prepare aconstruct for PCR amplification.

In a further embodiment, adaptor arm A used in an arm-by-arm ligationreaction can be designed for direct circularization without PCR,followed by nick translation ligation to seal the circle. In anexemplary embodiment, for direct circularization, adaptor arm A can bedesigned as pictured in FIG. 11B. Segment 1101 is designed to becomplementary to adaptor arm B. The construct in FIG. 11B allows fordirect primer extension by a strand displacing polymerase (such asphi29) without a need for a primer exchange reaction to remove a blockedend (the polymerase will not extend past the 3′ phosphate on segment1102). This construct also provides a 3′ overhang for circularization.Segment 1102 prevents hybridization of adaptor arm A to adaptor arm Bbefore circularization. In some embodiments, segment 1102 may not benecessary for preventing hybridization to arm B (such as when adaptorarm B is provided in very high concentrations) or segment 1102 may bepart of the design of adaptor arm B rather than adaptor arm A.

After generating the single stranded 3′ ends, a second adaptor 1803 ishybridized to the single stranded 3′ end of the target nucleic acid andconnected to the first adaptor through a nick translation ligationreaction (in one embodiment, the nick translation ligation is a “primerextension” or “gap fill-in” reaction). The second adaptor has a 5′phosphate and a 3′ block (identified as the vertical line 1804). The 3′block can in some embodiments be a removable block such as a 3′phosphate, which can be removed in some exemplary embodiments usingpolynucleotide kinase (PNK) and/or shrimp alkaline phosphate. The secondadaptor may in some embodiments have degenerated bases at the 3′ and/orthe 5′ ends. In some exemplary embodiments, the second adaptor has about2-6 degenerated bases at the 5′ end and 4-9 degenerated bases at the 3′end, although it will be appreciated that any combination of numbers ofdegenerated bases at one or both ends of the second adaptor areencompassed by the present invention. In the embodiment pictured in FIG.18, the second adaptor comprises 3 degenerate bases at the 5′ end (“N3”)and 7 degenerate bases at its 3′ end (“N7”). The joining of the firstadaptor to the second adaptor may in some embodiments be accomplishedunder reaction conditions at which hybridization of the adaptors to thetarget nucleic acid are favored. In some exemplary embodiments, suchreaction conditions may include temperatures of from about 20 to about40° C. Polymerases that can be used under such reaction conditionsinclude without limitations phi29, Klenow, T4 polymerases and Pol I.

The ligation product 1805 is then denatured and/or further processedwith a 5′-3′ exonucleases followed by a re-annealing step to form twosingle stranded nucleic acid molecules (denoted by the “x2” in FIG. 18).During re-annealing, the N7 part of the second adaptor may hybridize toa segment at a random distance from the first hybridization sequencemotif, thereby forming a single stranded loop 1806. In some embodiments,the N7 end of the second adaptor may not hybridize until denaturationproduces long single stranded regions of the nucleic acid 1807. Theaverage distance between two captured genomic segments (which aregenerally from about 20 to about 200 bases in length) will in manyembodiments be between about 0.5 to about 20 kilobases. This averagedistance will depend in part on the number of degenerate bases (“Ns”) ofthe adaptors and the stringency of hybridization conditions. There-annealing step can then be followed by another round of adaptorhybridization and nick translation ligation. A final adaptor (in FIG.18, this final adaptor is pictured as a third adaptor 1808, but it willbe appreciated that the final adaptor may be the fourth, fifth, sixth,seventh or more adaptor inserted according to any of the methodsdescribed herein) is similar to the second adaptor but will in manyembodiments lack the degenerate bases at the 3′ end. In furtherembodiments, the final adaptor may comprise a binding site for a primerfor an amplification reaction, for example a PCR primer.

In still further embodiments, amplification reactions, such as PCRreactions (see 1809 in FIG. 18), can be carried out, for example, byusing primer binding sites included in the first and final adaptors. Instill further embodiments, the first and final adaptors may be two armsof the same adaptor and more than one adaptor may be inserted prior tothe addition of the final adaptor. In a yet further embodiment, theamplification products may be used to form circular double strandednucleic acid molecules for further adaptor insertion using any of theprocess described herein or known in the art.

IVD(iii). Controlled Insertion of Subsequent Adaptors: Protection ofRestriction Endonuclease Recognition Sites

In addition to controlling the orientation of adaptors inserted into atarget nucleic acid as described above, multiple adaptors can also beinserted into a target nucleic acid at specified locations relative topreviously inserted adaptors. Such methods include embodiments in whichcertain restriction endonuclease recognition sites, particularlyrecognition sites contained in a previously inserted adaptor, areprotected from inactivation. In order to ligate subsequent adaptors in adesired position and orientation, the present invention provides methodsin which a Type IIs restriction endonuclease binds to a recognition sitewithin the first adaptor of a circular nucleic acid construct and thencleaves at a point outside the first adaptor and in the genomic fragment(also referred to herein as the “target nucleic acid”). A second adaptorcan then be ligated into the point at which cleavage occurs (again,usually by adding two adaptor arms of the second adaptor). In order tocleave the target nucleic acid at a known point, it is necessary toblock any other recognition sites for that same enzyme that may randomlybe encompassed in the target nucleic acid, such that the only point atwhich that restriction endonuclease can bind is within the firstadaptor, thus avoiding undesired cleavage of the constructs. Generally,the recognition site in the first adaptor is first protected frominactivation, and then any other unprotected recognition sites in theconstruct are inactivated, generally through methylation. By“inactivation” of a restriction endonuclease recognition site herein ismeant that the recognition site is somehow rendered unavailable forbinding by a restriction endonuclease, thus preventing the downstreamstep of cleavage by that enzyme. For example, methylated recognitionsites will not bind the restriction endonuclease, and thus no cleavagewill occur. Once all recognition sites in a nucleic acid construct thatare unprotected have been methylated, only the unmethylated recognitionsite within the adaptor will allow binding of the enzyme with subsequentcleaving. Other methods of inactivating recognition sites includewithout limitation applying a methylase block to the recognition site,using a blocking oligonucleotide to block the recognition site, usingsome other blocking molecule, such as a zinc finger protein, to blockthe recognition site, and nicking the recognition site to preventmethylation. Such methods for protecting the desired recognition siteare described in U.S. application Ser. Nos. 12/265,593, filed Nov. 5,2008 and 12/266,385, filed Nov. 6, 2008, which are both hereinincorporated by reference in their entirety and for all purposes and inparticular for all teachings related to inserting multiple interspersedadaptors into a target nucleic acid.

It will be appreciated that the methods described above for controllingthe orientation in which adaptors and target nucleic acids ligate toeach other may also be used in combination with the methods describedbelow for controlling the spacing of each subsequently added adaptor.

In one aspect, the present invention provides a method of protecting therecognition site in the first adaptor from inactivation by rendering therecognition site in the first adaptor single-stranded, such that amethylase that is only able to methylate double-stranded molecules willbe unable to methylate the recognition site being protected. One methodof rendering the recognition site in the first adaptor single-strandedis by amplifying the linear genomic fragments ligated to the two firstadaptor arms using primers modified with uracil. The primers arecomplementary to the adaptor arms and are modified with uracil suchthat, upon amplification (generally using PCR), the resultant linearconstructs contain uracil embedded in the recognition site of one of thefirst adaptor arms. The primers generate a PCR product with uracilsclose to the Type IIs restriction endonuclease recognition site in thefirst and/or second arms of the first adaptor. Digestion of the uracilrenders the region(s) of the adaptor arm that include the Type IIsrecognition site to be protected single stranded. A sequence specificmethylase is then applied to the linear constructs that will methylateall of the double-stranded recognition sites for the same endonucleaseas that contained in the first adaptor. Such a sequence-specificmethylase will not be able to methylate the single stranded recognitionsite in the first adaptor arm(s), and thus the recognition site in thefirst adaptor arm(s) will be protected from inactivation by methylation.

In some cases, as more fully described below, a single adaptor may havetwo of the same recognition sites, to allow cleavage both “upstream” and“downstream” from the same adaptor. In this embodiment, as depicted inFIG. 7, the primers and uracil positions are chosen appropriately, suchthat either the “upstream” or “downstream” recognition site may beselectively protected from inactivation or inactivated.

A third adaptor can be inserted on the other side of the first adaptorby cutting with a restriction endonuclease bound to a recognition sitein the second arm of the first adaptor (the recognition site that wasoriginally inactivated by methylation). In order to make thisrecognition site available, uracil-modified primers complementary to thesecond recognition site in the first adaptor are used to amplify thecircular constructs to produce third linear constructs in which thefirst adaptor comprises uracils embedded in the second restrictionrecognition site. The uracils are degraded to render the first adaptorsingle stranded, which protects the recognition site in the adaptor frommethylation. Applying a sequence-specific methylase will then inactivateall unprotected recognition sites. Upon circularization the recognitionsite in the first adaptor is reconstituted, and applying the restrictionendonuclease will cleave the circle, producing a position at which thethird adaptor can be inserted in a third linear construct. Ligatingthird adaptor arms to the third linear construct will follow the samegeneral procedure described above—the third linear construct will be A-or G-tailed, the third adaptor arms will be T- or C-tailed, allowing theadaptor arms to anneal to the third linear construct and be ligated. Thelinear construct comprising the third adaptor arms is then circularizedto form a third circular construct. Like the second adaptor, the thirdadaptor will generally comprise a recognition site for a restrictionendonuclease that is different than the recognition site contained inthe first adaptor.

A fourth adaptor can be added by utilizing Type IIs restrictionendonucleases that have recognition sites in the second and thirdadaptors. Cleavage with these restriction endonucleases will result in afourth linear construct that can then be ligated to fourth adaptor arms.Circularization of the fourth linear construct ligated to the fourthadaptor arms will produce the nucleic acid template constructs of theinvention.

In general, methods of the invention provide a way to specificallyprotect a Type IIs endonuclease recognition site from inactivation suchthat, once all remaining unprotected recognition sites in a constructare inactivated, application of the Type IIs endonuclease will result inbinding only to the protected site, thus providing control over wherethe subsequent cleavage occurs in the construct. The method describedabove provides one embodiment of how to protect the desired recognitionsite from inactivation. It will be appreciated that the above-describedmethod can be modified using techniques known in the art, and that suchmodified methods are encompassed by the present invention.

In one exemplary embodiment, each subsequently inserted adaptor isinserted using a method in which a recognition site is protected frominactivation using a combination of methods. FIG. 19 is a schematicillustration of an embodiment in which a second adaptor is inserted at adesired position relative to a first adaptor by employing a process thatis a combination of methylation and protection from methylation using acombination of uracil degradation and nickase. FIG. 19 shows genomic DNAof interest 1902 having a Type IIs restriction endonuclease recognitionsite at 1904. The genomic DNA is fractionated or fragmented in process1905 to produce fragment 1906 having a Type IIs restriction endonucleaserecognition site 1904. Adaptor arms 1908 and 1910 are ligated tofragment 1906 in process 1907. Fragment 1906 with first and secondadaptor arms 1908 and 1910 (a library construct) are amplified by PCR inprocess 1911, using uracil-modified primers 1912 complementary toadaptor arms 1908 and 1910. The primers generate a PCR product withuracils close to the Type IIs restriction endonuclease recognition site.In process 1913, the uracils are specifically degraded using, e.g.,uracil-DNA glycosylase enzyme (Krokan, et al., (1997) Biochem. J.325:1-16), leaving a PCR product that is single-stranded in the Type IIsrestriction endonuclease recognition site region. As shown, uracilincorporation and degradation may be used to render the Type IIsrestriction endonuclease recognition site single-stranded; however, asdescribed further herein, other methods may be employed to render theseregions single-stranded including use of 3′ or 5′ exonucleases in alimited digest.

In process 1915, a sequence-specific nickase is used to nick bases ineach double-stranded Type IIs restriction endonuclease recognition siteto protect these sites from Type IIs restriction endonucleaserecognition. However, the single-stranded Type IIs restrictionendonuclease recognition site portions in first and second adaptor arms1908 and 1910 will not be nicked, and, once circularized and ligated1917, the Type IIs restriction endonuclease recognition site in thefirst and second adaptor arms re-forms such that this Type IIsrestriction endonuclease recognition site is available for restriction.When selecting the nickase and the Type IIs restriction endonucleasesfor this process, it is preferred that the two enzymes recognize thesame sequence or that one enzyme recognizes a subsequence (sequencewithin the sequence) of the other enzyme. Alternatively, the nickase mayrecognize a different sequence, but is positioned within the adaptor sothat it nicks in the Type IIs restriction endonuclease recognition site.Use of uracil or 3′ or 5 degradation permits the use of one nickaseenzyme throughout the process; alternatively, more than onesequence-specific nickase may be employed. The circularized construct isthen cut with the Type IIs restriction endonuclease in process 1919where the Type IIs restriction endonuclease recognition site isindicated at 1922, the construct is cut at 1920, and the nick isindicated at 1918, resulting in a linearized construct available forligation of a second set of adaptor arms to be added to the construct inprocess 1921

Ligation process 1921 adds first 1924 and second 1926 adaptor arms ofthe second adaptor to the linearized construct, and a secondamplification is performed by PCR at process 1923, again usinguracil-modified primers 1928 complementary to adaptor arms 1924 and1926. As before, the primers generate a PCR product with uracils closeto the Type IIs restriction endonuclease recognition site. In process1925, the uracils are specifically degraded leaving a PCR product thatis single-stranded in the Type IIs restriction endonuclease recognitionsite region of the first and second adaptor arms 1924 and 1926 of thesecond adaptor. Ligation process 1921 also serves to repair the nick1918 in the Type IIs restriction site 1904 in the target nucleic acidfragment 1906. In process 1927, the sequence-specific nickase again isused to nick bases in the double-stranded Type IIs restrictionendonuclease recognition sites in the target nucleic acid fragment(there is nicking 1914 of the Type IIs restriction endonucleaserecognition site 1904) and in the Type IIs restriction endonucleaserecognition site of the first adaptor 1930 protecting these sites fromType IIs restriction endonuclease recognition.

The nicked construct is then circularized and ligated at process 1929,where the Type IIs restriction endonuclease recognition site in thefirst and second arms 1924 and 1926 of the second adaptor is re-formed1932 and the process is repeated where the circularized construct is cutagain with the Type IIs restriction endonuclease in process 1931 togenerate another linearized construct (this one with first and secondadaptors already added) available for ligation of a third pair ofadaptor arms 1936 and 1938 to the construct. The Type IIs restrictionendonuclease recognition site is shown at 1922, the site of restrictionis shown at 1920, the nick Type IIs restriction endonuclease recognitionsite in the target nucleic acid fragment is shown at 1918 and the nickin the first adaptor is shown at 1934. The process can be repeated toadd as many adaptors as are desired. As shown here, the first addedadaptor had one Type IIs restriction endonuclease recognition site;however, in other aspects, the first added adaptor may have two Type IIsrestriction endonuclease recognition sites to allow for preciseselection of target nucleic acid size for the construct.

In one aspect, adaptors can be designed to have sequence-specificnickase sites surrounding or partially overlapping the Type IIsrestriction endonuclease recognition site. By utilizing the nickase, theType IIs restriction endonuclease recognition site(s) of each adaptorcan be selectively protected from methylation. In further embodiments,the nickase may recognize another sequence or site, but will cut at theType IIs restriction endonuclease recognition site. Nickases areendonucleases recognize a specific recognition sequence indouble-stranded DNA, and cut one strand at a specific location relativeto the recognition sequence, thereby giving rise to single-strandedbreaks in duplex DNA and include but are not limited to Nb.BsrDI,Nb.BsmI, Nt.BbvCI, Nb.Bbv.Nb.BtsI and Nt.BstNBI. By employing acombination of sequence-specific nickase and Type IIs restrictionendonuclease, all Type IIs restriction endonuclease recognition sites inthe target nucleic acid as well as the Type IIs restriction endonucleaserecognition sites in any previously-inserted adaptor can be protectedfrom digestion (assuming, of course, the Type IIs restrictionendonuclease is nick sensitive, i.e., will not bind at a recognitionsite that has been nicked).

FIG. 20 is a schematic representation of an embodiment of methods of theinvention where a desired position of a second adaptor relative to afirst adaptor is selected using methylation and sequence-specificnickases. FIG. 20 shows genomic DNA of interest (target nucleic acid)2002 having a Type IIs restriction endonuclease recognition site at2004. The genomic DNA is fractionated or fragmented in process 2005 toproduce fragments 2006 having a Type IIs restriction endonucleaserecognition site 2004. Adaptor arms 2008 and 2010 are ligated tofragment 2006 in process 2007. Fragment 2006 with adaptor arms 2008 and2010 (a library construct) is circularized in process 2009 and amplifiedby circle dependent amplification in process 2011, resulting in ahighly-branched concatemer of alternating target nucleic acid fragments2006 (with the Type IIs restriction endonuclease recognition site at2004) and first adaptors 2012.

In process 2013, a sequence-specific nickase 2030 is used to nick thenucleic acid in or near specific Type IIs restriction endonucleaserecognition sites in the adaptor in the library construct therebyblocking methylation of these sites. Here, the Type IIs restrictionendonuclease recognition sites in adaptor arms 2012 and 2014 are nickedby sequence-specific nickase 2030. In process 2015, un-nicked Type IIsrestriction endonuclease recognition sites in the construct aremethylated—here, methylation 2016 of the Type IIs restrictionendonuclease recognition site 2004)—protecting these sites from Type IIsrestriction endonuclease recognition. However, the Type IIs restrictionendonuclease recognition sites in adaptors 2012 and 2014 are notmethylated due to the presence of the nicks.

At process 2017, the nicks are repaired in the library construct,resulting in a library construct where the Type IIs restrictionendonuclease recognition site in adaptors 2012 are available forrecognition and restriction 2018, and the Type IIs restrictionendonuclease recognition site in the genomic fragment 2004, is not. Themethylated construct is then ligated to an second pair of adaptor arms,circularized, and amplified via circle dependent amplification atprocess 2021, resulting in a concatemer of alternating target nucleicacid fragments 2006 (with the Type IIs restriction endonucleaserecognition site at 2004), first adaptors 2012 and second adaptors 2020.Next, in process 2023, sequence-specific nicking is performed again,this time with a sequence-specific nickase that recognizes a site in thesecond adaptor 2020 to block methylation of the Type IIs restrictionendonuclease recognition site in the second adaptor 2020, but not theother Type IIs restriction endonuclease recognition sites in theconstruct (i.e., the Type IIs restriction endonuclease recognition site2004 in the fragment and the Type IIs restriction endonucleaserecognition site in first adaptor 2012). The process then continues withmethylation 2015, and further adaptor arms are added, if desired.Different sequence-specific nickase sites are used in each differentadaptor, allowing for sequence-specific nicking throughout the process.

FIG. 21 is a schematic representation of a process where a desiredposition of a second adaptor relative to a first adaptor is selectedusing methylation and sequence-specific methylase blockers. FIG. 21shows genomic DNA of interest (target nucleic acid) 2212 having a TypeIIs restriction endonuclease recognition site at 2214. The genomic DNAis fractionated or fragmented in process 2105 to produce fragment 2106having a Type IIs restriction endonuclease recognition site 2104.Adaptor arms 2108 and 2110 are ligated to fragment 2106 in process 2107.Fragment 2106 with adaptor arms 2108 and 2110 (a library construct) iscircularized in process 2109 and amplified by circle dependentamplification in process 2111, resulting in a highly-branched concatemerof alternating target nucleic acid fragments 2106 (with the Type IIsrestriction endonuclease recognition site at 2104) and first adaptors2112.

In process 2113, a sequence-specific methylase blocker 2130 such as azinc finger is used to block methylation in specific Type IIsrestriction endonuclease recognition sites in the library construct.Here, the Type IIs restriction endonuclease recognition sites in adaptorarms 2112 and 2114 are blocked by methylase blocker 2130. When selectingthe methylase blocker and the Type IIs restriction endonucleases forthis process, it is not necessary that the two entities recognize thesame site sequence or that one entity recognizes a subsequence of theother entity. The blocker sequences may be up- or downstream from theType IIs restriction endonuclease recognition site, but are of aconfiguration that the methylase blocker blocks the site (such as with azinc finger or other nucleic acid binding protein or other entity). Inprocess 2115, unprotected Type IIs restriction endonuclease recognitionsites in the construct are methylated—here, methylation 2116 of the TypeIIs restriction endonuclease recognition site 2104)—protecting thesesites from Type IIs restriction endonuclease recognition. However, theType IIs restriction endonuclease recognition sites in adaptors 2112 and2114 are not methylated due to the presence of the methylase blocker.

At process 2117, the methylase blocker is released from the libraryconstruct, resulting in a library construct where the Type IIsrestriction endonuclease recognition site in adaptors 2112 are availablefor recognition and restriction 2118, and the Type IIs restrictionendonuclease recognition site in the genomic fragment 2104, is not. Themethylated construct is then ligated to an second pair of adaptor arms,circularized, and amplified via circle dependent amplification atprocess 2121, resulting in a concatemer of alternating target nucleicacid fragments 2106 (with the Type IIs restriction endonucleaserecognition site at 2104), first adaptors 2112 and second adaptors 2120.Next, in process 2123, methylase blocking is performed again, this timewith a methylase blocker that recognizes a site in the second adaptor2120 to block methylation of the Type IIs restriction endonucleaserecognition site in the second adaptor 2120, but not the other Type IIsrestriction endonuclease recognition sites in the construct (i.e., theType IIs restriction endonuclease recognition site 2104 in the fragmentand the Type IIs restriction endonuclease recognition site in firstadaptor 2112). The process then continues with methylation 2115, andfurther adaptor arms are added, if desired. Different methylase blockersites are used in each different adaptor, allowing for sequence-specificmethylase blocking throughout the process. Though FIGS. 9 and 21 showinsertion of a second adaptor in relation to a first, it should beunderstood that the process is applicable to adaptors added subsequentlyto the second adaptor, creating library constructs with up to four, six,eight, ten or more inserted adaptors.

FIG. 22 is a schematic illustration of a process where a desiredposition of a second adaptor relative to a first adaptor is selectedusing methylation and uracil degradation. FIG. 22 shows genomic DNA ofinterest 2202 having a Type IIs restriction endonuclease recognitionsite at 2204. The genomic DNA is fractionated or fragmented in process2205 to produce fragments 2206 having a Type IIs restrictionendonuclease recognition site 2204. Adaptor arms 2208 and 2210 areligated to fragment 2206 in process 2207. Fragment 2206 with first andsecond adaptor arms 2208 and 2210 (a library construct) are amplified byPCR in process 2211, using uracil-modified primers 2212 complementary toadaptor arms 2208 and 2210. The primers generate a PCR product withuracils at or close to the Type IIs restriction endonuclease recognitionsite. In process 2213, the uracils are specifically degraded using,e.g., uracil-DNA glycosylase enzyme (Krokan, et al., (1997) Biochem. J.325:1-16), leaving a PCR product that is single-stranded in the Type IIsrestriction endonuclease recognition site region. As shown, uracilincorporation and degradation may be used to render the Type IIsrestriction endonuclease recognition site single-stranded; however, asdescribed further herein, other methods may be employed to render theseregions single-stranded including use of 3′ or 5′ exonucleases in alimited digest.

In process 2215, a sequence-specific methylase is used to methylatebases in each double-stranded Type IIs restriction endonucleaserecognition site (here, there is methylation 2214 of the Type IIsrestriction endonuclease recognition site 2204), to protect these sitesfrom Type IIs restriction endonuclease recognition. However, thesingle-stranded Type IIs restriction endonuclease recognition sites infirst and second adaptor arms 2208 and 2210 are not methylated, and,once circularized and ligated 2217, the Type IIs restrictionendonuclease recognition site re-forms 2216 such that this Type IIsrestriction endonuclease recognition site is available for restriction.When selecting the methylase and the Type IIs restriction endonucleasesfor this process, it is necessary that the two enzymes recognize thesame sequence or that one enzyme recognizes a subsequence (sequencewithin the sequence) of the other enzyme. The circularized construct isthen cut with the Type IIs restriction endonuclease in process 2219where the Type IIs restriction endonuclease recognition site isindicated at 2218 and the construct is cut at 2220, resulting in alinearized construct available for ligation of a second set of adaptorarms to be added to the construct in process 2221.

Ligation process 2221 adds first 2222 and second 2224 adaptor arms ofthe second adaptor to the linearized construct, and a secondamplification is performed by PCR at process 2223, again usinguracil-modified primers 2226 complementary to adaptor arms 2222 and2224. As before, the primers generate a PCR product with uracils closeto the Type IIs restriction endonuclease recognition site. In process2225, the uracils are specifically degraded leaving a PCR product thatis single-stranded in the Type IIs restriction endonuclease recognitionsite region of the first and second adaptor arms 2222 and 2224 of thesecond adaptor. In process 2227, the sequence-specific methylase againis used to methylate bases in the double-stranded Type IIs restrictionendonuclease recognition sites in the target nucleic acid fragment(again, there is methylation 2214 of the Type IIs restrictionendonuclease recognition site 2204) and in the Type IIs restrictionendonuclease recognition site of the first adaptor 2228 protecting thesesites from Type IIs restriction endonuclease recognition. The methylatedconstruct is then circularized at process 2229, where the Type IIsrestriction endonuclease recognition site in the first and second arms2222 and 2224 of the second adaptor is re-formed 2230 and the process isrepeated where the circularized construct is cut again with the Type IIsrestriction endonuclease in process 2219 to generate another linearizedconstruct (this one with first and second adaptors already added)available for ligation of a third pair of adaptor arms to the construct.The process can be repeated to add as many adaptors as are desired. Asshown here, the first added adaptor had one Type IIs restrictionendonuclease recognition site; however, in other aspects, the firstadded adaptor may have two Type IIs restriction endonuclease recognitionsites to allow for precise selection of target nucleic acid size for theconstruct.

In addition to the above methods for controlled insertion of multipleinterspersed adaptors, constructs comprising adaptors in specificorientations may further be selected by enriching a population ofconstructs for those with adaptors in the desired orientations. Suchenrichment methods are described in U.S. Ser. Nos. 60/864,992 filed Nov.9, 2006; 11/943,703, filed Nov. 2, 2007; 11/943,697, filed Nov. 2, 2007;11/943,695, filed Nov. 2, 2007; and PCT/US07/835,540; filed Nov. 2,2007, all of which are incorporated by reference in their entirety forall purposes and in particular for all teachings related to methods andcompositions for selecting for specific orientations of adaptors.

V. Making DNBs

In one aspect, nucleic acid templates of the invention are used togenerate nucleic acid nanoballs, which are also referred to herein as“DNA nanoballs,” “DNBs”, and “amplicons”. These nucleic acid nanoballsare generally concatemers comprising multiple copies of a nucleic acidtemplate of the invention, although nucleic acid nanoballs of theinvention may be formed from any nucleic acid molecule using the methodsdescribed herein.

In one aspect, rolling circle replication (RCR) is used to createconcatemers of the invention. The RCR process has been shown to generatemultiple continuous copies of the M13 genome. (Blanco, et al., (1989) JBiol Chem 264:8935-8940). In such a method, a nucleic acid is replicatedby linear concatemerization. Guidance for selecting conditions andreagents for RCR reactions is available in many references available tothose of ordinary skill, including U.S. Pat. Nos. 5,426,180; 5,854,033;6,143,495; and 5,871,921, each of which is hereby incorporated byreference in its entirety for all purposes and in particular for allteachings related to generating concatemers using RCR or other methods.

Generally, RCR reaction components include single stranded DNA circles,one or more primers that anneal to DNA circles, a DNA polymerase havingstrand displacement activity to extend the 3′ ends of primers annealedto DNA circles, nucleoside triphosphates, and a conventional polymerasereaction buffer. Such components are combined under conditions thatpermit primers to anneal to DNA circle. Extension of these primers bythe DNA polymerase forms concatemers of DNA circle complements. In someembodiments, nucleic acid templates of the invention are double strandedcircles that are denatured to form single stranded circles that can beused in RCR reactions.

In some embodiments, amplification of circular nucleic acids may beimplemented by successive ligation of short oligonucleotides, e.g.,6-mers, from a mixture containing all possible sequences, or if circlesare synthetic, a limited mixture of these short oligonucleotides havingselected sequences for circle replication, a process known as “circledependent amplification” (CDA). “Circle dependant amplification” or“CDA” refers to multiple displacement amplification of a double-strandedcircular template using primers annealing to both strands of thecircular template to generate products representing both strands of thetemplate, resulting in a cascade of multiple-hybridization,primer-extension and strand-displacement events. This leads to anexponential increase in the number of primer binding sites, with aconsequent exponential increase in the amount of product generated overtime. The primers used may be of a random sequence (e.g., randomhexamers) or may have a specific sequence to select for amplification ofa desired product. CDA results in a set of concatemeric double-strandedfragments being formed.

Concatemers may also be generated by ligation of target DNA in thepresence of a bridging template DNA complementary to both beginning andend of the target molecule. A population of different target DNA may beconverted in concatemers by a mixture of corresponding bridgingtemplates.

In some embodiments, a subset of a population of nucleic acid templatesmay be isolated based on a particular feature, such as a desired numberor type of adaptor. This population can be isolated or otherwiseprocessed (e.g., size selected) using conventional techniques, e.g., aconventional spin column, or the like, to form a population from which apopulation of concatemers can be created using techniques such as RCR.

Methods for forming DNBs of the invention are described in PublishedPatent Application Nos. WO2007120208, WO2006073504, WO2007133831, andUS2007099208, and U.S. Patent Application Nos. 60/992,485; 61/026,337;61/035,914; 61/061,134; 61/116,193; 61/102,586; 12/265,593; 12/266,385;11/938,096; 11/981,804; Ser. Nos. 11/981,797; 11/981,793; 11/981,767;11/981,761; 11/981,730, filed Oct. 31, 2007; 11/981,685; 11/981,661;11/981,607; 11/981,605; 11/927,388; 11/927,356; 11/679,124; 11/541,225;10/547,214; 11/451,692; and 11/451,691, all of which are incorporatedherein by reference in their entirety for all purposes and in particularfor all teachings related to forming DNBs.

VI. Producing Arrays of DNBs

In one aspect, DNBs of the invention are disposed on a surface to form arandom array of single molecules. DNBs can be fixed to surface by avariety of techniques, including covalent attachment and non-covalentattachment. In one embodiment, a surface may include capture probes thatform complexes, e.g., double stranded duplexes, with component of apolynucleotide molecule, such as an adaptor oligonucleotide. In otherembodiments, capture probes may comprise oligonucleotide clamps, or likestructures, that form triplexes with adaptors, as described in Gryaznovet al, U.S. Pat. No. 5,473,060, which is hereby incorporated in itsentirety.

Methods for forming arrays of DNBs of the invention are described inPublished Patent Application Nos. WO2007120208, WO2006073504,WO2007133831, and US2007099208, and U.S. Patent Application Nos.60/992,485; 61/026,337; 61/035,914; 61/061,134; 61/116,193; 61/102,586;12/265,593; 12/266,385; 11/938,096; 11/981,804; No. 11/981,797;11/981,793; 11/981,767; 11/981,761; 11/981,730; 11/981,685; 11/981,661;11/981,607; 11/981,605; 11/927,388; 11/927,356; 11/679,124; 11/541,225;10/547,214; 11/451,692; and 11/451,691, all of which are incorporatedherein by reference in their entirety for all purposes and in particularfor all teachings related to forming arrays of DNBs.

In some embodiments, a surface may have reactive functionalities thatreact with complementary functionalities on the polynucleotide moleculesto form a covalent linkage, e.g., by way of the same techniques used toattach cDNAs to microarrays, e.g., Smirnov et al (2004), Genes,Chromosomes & Cancer, 40: 72-77; Beaucage (2001), Current MedicinalChemistry, 8: 1213-1244, which are incorporated herein by reference.DNBs may also be efficiently attached to hydrophobic surfaces, such as aclean glass surface that has a low concentration of various reactivefunctionalities, such as —OH groups. Attachment through covalent bondsformed between the polynucleotide molecules and reactive functionalitieson the surface is also referred to herein as “chemical attachment”.

In still further embodiments, polynucleotide molecules can adsorb to asurface. In such an embodiment, the polynucleotide molecules areimmobilized through non-specific interactions with the surface, orthrough non-covalent interactions such as hydrogen bonding, van derWeals forces, and the like.

Attachment may also include wash steps of varying stringencies to removeincompletely attached single molecules or other reagents present fromearlier preparation steps whose presence is undesirable or that arenonspecifically bound to surface.

In one aspect, DNBs on a surface are confined to an area of a discreteregion. Discrete regions may be incorporated into a surface usingmethods known in the art and described further herein. In exemplaryembodiments, discrete regions contain reactive functionalities orcapture probes which can be used to immobilize the polynucleotidemolecules.

The discrete regions may have defined locations in a regular array,which may correspond to a rectilinear pattern, hexagonal pattern, or thelike. A regular array of such regions is advantageous for detection anddata analysis of signals collected from the arrays during an analysis.Also, first- and/or second-stage amplicons confined to the restrictedarea of a discrete region provide a more concentrated or intense signal,particularly when fluorescent probes are used in analytical operations,thereby providing higher signal-to-noise values. In some embodiments,DNBs are randomly distributed on the discrete regions so that a givenregion is equally likely to receive any of the different singlemolecules. In other words, the resulting arrays are not spatiallyaddressable immediately upon fabrication, but may be made so by carryingout an identification, sequencing and/or decoding operation. As such,the identities of the polynucleotide molecules of the invention disposedon a surface are discernable, but not initially known upon theirdisposition on the surface. In some embodiments, the area of discrete isselected, along with attachment chemistries, macromolecular structuresemployed, and the like, to correspond to the size of single molecules ofthe invention so that when single molecules are applied to surfacesubstantially every region is occupied by no more than one singlemolecule. In some embodiments, DNBs are disposed on a surface comprisingdiscrete regions in a patterned manner, such that specific DNBs(identified, in an exemplary embodiment, by tag adaptors or otherlabels) are disposed on specific discrete regions or groups of discreteregions.

In some embodiments, the area of discrete regions is less than 1 μm²;and in some embodiments, the area of discrete regions is in the range offrom 0.04 μm² to 1 μm²; and in some embodiments, the area of discreteregions is in the range of from 0.2 μm² to 1 μm². In embodiments inwhich discrete regions are approximately circular or square in shape sothat their sizes can be indicated by a single linear dimension, the sizeof such regions are in the range of from 125 nm to 250 nm, or in therange of from 200 nm to 500 nm. In some embodiments, center-to-centerdistances of nearest neighbors of discrete regions are in the range offrom 0.25 μm to 20 μm; and in some embodiments, such distances are inthe range of from 1 μm to 10 μm, or in the range from 50 to 1000 nm.Generally, discrete regions are designed such that a majority of thediscrete regions on a surface are optically resolvable. In someembodiments, regions may be arranged on a surface in virtually anypattern in which regions have defined locations.

In further embodiments, molecules are directed to the discrete regionsof a surface, because the areas between the discrete regions, referredto herein as “inter-regional areas,” are inert, in the sense thatconcatemers, or other macromolecular structures, do not bind to suchregions. In some embodiments, such inter-regional areas may be treatedwith blocking agents, e.g., DNAs unrelated to concatemer DNA, otherpolymers, and the like.

A wide variety of supports may be used with the compositions and methodsof the invention to form random arrays. In one aspect, supports arerigid solids that have a surface, preferably a substantially planarsurface so that single molecules to be interrogated are in the sameplane. The latter feature permits efficient signal collection bydetection optics, for example. In another aspect, the support comprisesbeads, wherein the surface of the beads comprise reactivefunctionalities or capture probes that can be used to immobilizepolynucleotide molecules.

In still another aspect, solid supports of the invention are nonporous,particularly when random arrays of single molecules are analyzed byhybridization reactions requiring small volumes. Suitable solid supportmaterials include materials such as glass, polyacrylamide-coated glass,ceramics, silica, silicon, quartz, various plastics, and the like. Inone aspect, the area of a planar surface may be in the range of from 0.5to 4 cm². In one aspect, the solid support is glass or quartz, such as amicroscope slide, having a surface that is uniformly silanized. This maybe accomplished using conventional protocols, e.g., acid treatmentfollowed by immersion in a solution of 3-glycidoxypropyltrimethoxysilane, N,N-diisopropylethylamine, and anhydrous xylene(8:1:24 v/v) at 80° C., which forms an epoxysilanized surface. e.g.,Beattie et al (1995), Molecular Biotechnology, 4: 213. Such a surface isreadily treated to permit end-attachment of capture oligonucleotides,e.g., by providing capture oligonucleotides with a 3′ or 5′ triethyleneglycol phosphoryl spacer (see Beattie et al, cited above) prior toapplication to the surface. Further embodiments for functionalizing andfurther preparing surfaces for use in the present invention aredescribed for example in U.S. Patent Application Ser. Nos. 60/992,485;61/026,337; 61/035,914; 61/061,134; 61/116,193; 61/102,586; 12/265,593;12/266,385; 11/938,096; 11/981,804; No. 11/981,797; 11/981,793;11/981,767; 11/981,761; 11/981,730; 11/981,685; 11/981,661; 11/981,607;11/981,605; 11/927,388; 11/927,356; 11/679,124; 11/541,225; 10/547,214;11/451,692; and 11/451,691, each of which is herein incorporated byreference in its entirety for all purposes and in particular for allteachings related to preparing surfaces for forming arrays and for allteachings related to forming arrays, particularly arrays of DNBs.

In embodiments of the invention in which patterns of discrete regionsare required, photolithography, electron beam lithography, nano imprintlithography, and nano printing may be used to generate such patterns ona wide variety of surfaces, e.g., Pirrung et al, U.S. Pat. No.5,143,854; Fodor et al, U.S. Pat. No. 5,774,305; Guo, (2004) Journal ofPhysics D: Applied Physics, 37: R123-141; which are incorporated hereinby reference.

In one aspect, surfaces containing a plurality of discrete regions arefabricated by photolithography. A commercially available, opticallyflat, quartz substrate is spin coated with a 100-500 nm thick layer ofphoto-resist. The photo-resist is then baked on to the quartz substrate.An image of a reticle with a pattern of regions to be activated isprojected onto the surface of the photo-resist, using a stepper. Afterexposure, the photo-resist is developed, removing the areas of theprojected pattern which were exposed to the UV source. This isaccomplished by plasma etching, a dry developing technique capable ofproducing very fine detail. The substrate is then baked to strengthenthe remaining photo-resist. After baking, the quartz wafer is ready forfunctionalization. The wafer is then subjected to vapor-deposition of3-aminopropyldimethylethoxysilane. The density of the aminofunctionalized monomer can be tightly controlled by varying theconcentration of the monomer and the time of exposure of the substrate.Only areas of quartz exposed by the plasma etching process may reactwith and capture the monomer. The substrate is then baked again to curethe monolayer of amino-functionalized monomer to the exposed quartz.After baking, the remaining photo-resist may be removed using acetone.Because of the difference in attachment chemistry between the resist andsilane, aminosilane-functionalized areas on the substrate may remainintact through the acetone rinse. These areas can be furtherfunctionalized by reacting them with p-phenylenediisothiocyanate in asolution of pyridine and N—N-dimethlyformamide. The substrate is thencapable of reacting with amine-modified oligonucleotides. Alternatively,oligonucleotides can be prepared with a 5′-carboxy-modifier-c10 linker(Glen Research). This technique allows the oligonucleotide to beattached directly to the amine modified support, thereby avoidingadditional functionalization steps.

In another aspect, surfaces containing a plurality of discrete regionsare fabricated by nano-imprint lithography (NIL). For DNA arrayproduction, a quartz substrate is spin coated with a layer of resist,commonly called the transfer layer. A second type of resist is thenapplied over the transfer layer, commonly called the imprint layer. Themaster imprint tool then makes an impression on the imprint layer. Theoverall thickness of the imprint layer is then reduced by plasma etchinguntil the low areas of the imprint reach the transfer layer. Because thetransfer layer is harder to remove than the imprint layer, it remainslargely untouched. The imprint and transfer layers are then hardened byheating. The substrate is then put into a plasma etcher until the lowareas of the imprint reach the quartz. The substrate is then derivatizedby vapor deposition as described above.

In another aspect, surfaces containing a plurality of discrete regionsare fabricated by nano printing. This process uses photo, imprint, ore-beam lithography to create a master mold, which is a negative image ofthe features required on the print head. Print heads are usually made ofa soft, flexible polymer such as polydimethylsiloxane (PDMS). Thismaterial, or layers of materials having different properties, are spincoated onto a quartz substrate. The mold is then used to emboss thefeatures onto the top layer of resist material under controlledtemperature and pressure conditions. The print head is then subjected toa plasma based etching process to improve the aspect ratio of the printhead, and eliminate distortion of the print head due to relaxation overtime of the embossed material. Random array substrates are manufacturedusing nano-printing by depositing a pattern of amine modifiedoligonucleotides onto a homogenously derivatized surface. Theseoligonucleotides would serve as capture probes for the RCR products. Onepotential advantage to nano-printing is the ability to print interleavedpatterns of different capture probes onto the random array support. Thiswould be accomplished by successive printing with multiple print heads,each head having a differing pattern, and all patterns fitting togetherto form the final structured support pattern. Such methods allow forsome positional encoding of DNA elements within the random array. Forexample, control concatemers containing a specific sequence can be boundat regular intervals throughout a random array.

In still another aspect, a high density array of capture oligonucleotidespots of sub micron size is prepared using a printing head orimprint-master prepared from a bundle, or bundle of bundles, of about10,000 to 100 million optical fibers with a core and cladding material.By pulling and fusing fibers a unique material is produced that hasabout 50-1000 nm cores separated by a similar or 2-5 fold smaller orlarger size cladding material. By differential etching (dissolving) ofcladding material a nano-printing head is obtained having a very largenumber of nano-sized posts. This printing head may be used fordepositing oligonucleotides or other biological (proteins,oligopeptides, DNA, aptamers) or chemical compounds such as silane withvarious active groups. In one embodiment the glass fiber tool is used asa patterned support to deposit oligonucleotides or other biological orchemical compounds. In this case only posts created by etching may becontacted with material to be deposited. Also, a flat cut of the fusedfiber bundle may be used to guide light through cores and allowlight-induced chemistry to occur only at the tip surface of the cores,thus eliminating the need for etching. In both cases, the same supportmay then be used as a light guiding/collection device for imagingfluorescence labels used to tag oligonucleotides or other reactants.This device provides a large field of view with a large numericalaperture (potentially >1). Stamping or printing tools that performactive material or oligonucleotide deposition may be used to print 2 to100 different oligonucleotides in an interleaved pattern. This processrequires precise positioning of the print head to about 50-500 nm. Thistype of oligonucleotide array may be used for attaching 2 to 100different DNA populations such as different source DNA. They also may beused for parallel reading from sub-light resolution spots by using DNAspecific anchors or tags. Information can be accessed by DNA specifictags, e.g., 16 specific anchors for 16 DNAs and read 2 bases by acombination of 5-6 colors and using 16 ligation cycles or one ligationcycle and 16 decoding cycles. This way of making arrays is efficient iflimited information (e.g., a small number of cycles) is required perfragment, thus providing more information per cycle or more cycles persurface.

In one aspect, multiple arrays of the invention may be placed on asingle surface. For example, patterned array substrates may be producedto match the standard 96 or 384 well plate format. A production formatcan be an 8×12 pattern of 6 mm×6 mm arrays at 9 mm pitch or 16×24 of3.33 mm×3.33 mm array at 4.5 mm pitch, on a single piece of glass orplastic and other optically compatible material. In one example each 6mm×6 mm array consists of 36 million 250-500 nm square regions at 1micrometer pitch. Hydrophobic or other surface or physical barriers maybe used to prevent mixing different reactions between unit arrays.

Other methods of forming arrays of molecules are known in the art andare applicable to forming arrays of DNBs.

As will be appreciated, a wide range of densities of DNBs and/or nucleicacid templates of the invention can be placed on a surface comprisingdiscrete regions to form an array. In some embodiments, each discreteregion may comprise from about 1 to about 1000 molecules. In furtherembodiments, each discrete region may comprise from about 10 to about900, about 20 to about 800, about 30 to about 700, about 40 to about600, about 50 to about 500, about 60 to about 400, about 70 to about300, about 80 to about 200, and about 90 to about 100 molecules.

In some embodiments, arrays of nucleic acid templates and/or DNBs areprovided in densities of at least 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10million molecules per square millimeter.

VII. Methods of Using DNBs

DNBs made according to the methods described above offer an advantage inidentifying sequences in target nucleic acids, because the adaptorscontained in the DNBs provide points of known sequence that allowspatial orientation and sequence determination when combined withmethods utilizing anchor and sequencing probes. Methods of using DNBs inaccordance with the present invention include sequencing and detectingspecific sequences in target nucleic acids (e.g., detecting particulartarget sequences (e.g. specific genes) and/or identifying and/ordetecting SNPs). The methods described herein can also be used to detectnucleic acid rearrangements and copy number variation. Nucleic acidquantification, such as digital gene expression (i.e., analysis of anentire transcriptome—all mRNA present in a sample) and detection of thenumber of specific sequences or groups of sequences in a sample, canalso be accomplished using the methods described herein. Although themajority of the discussion herein is directed to identifying sequencesof DNBs, it will be appreciated that other, non-concatemeric nucleicacid constructs comprising adaptors may also be used in the embodimentsdescribed herein.

VIIA. Overview of cPAL Sequencing

Sequences of DNBs are generally identified in accordance with thepresent invention using methods referred to herein as combinatorialprobe anchor ligation (“cPAL”) and variations thereof, as describedbelow. In brief, cPAL involves identifying a nucleotide at a particulardetection position in a target nucleic acid by detecting a probeligation product formed by ligation of at least one anchor probe thathybridizes to all or part of an adaptor and a sequencing probe thatcontains a particular nucleotide at an “interrogation position” thatcorresponds to (e.g. will hybridize to) the detection position. Thesequencing probe contains a unique identifying label. If the nucleotideat the interrogation position is complementary to the nucleotide at thedetection position, ligation can occur, resulting in a ligation productcontaining the unique label which is then detected. Descriptions ofdifferent exemplary embodiments of cPAL methods are provided below. Itwill be appreciated that the following descriptions are not meant to belimiting and that variations of the following embodiments areencompassed by the present invention.

“Complementary” or “substantially complementary” refers to thehybridization or base pairing or the formation of a duplex betweennucleotides or nucleic acids, such as, for instance, between the twostrands of a double-stranded DNA molecule or between an oligonucleotideprimer and a primer binding site on a single-stranded nucleic acid.Complementary nucleotides are, generally, A and T (or A and U), or C andG. Two single-stranded RNA or DNA molecules are said to be substantiallycomplementary when the nucleotides of one strand, optimally aligned andcompared and with appropriate nucleotide insertions or deletions, pairwith at least about 80% of the other strand, usually at least about 90%to about 95%, and even about 98% to about 100%.

As used herein, “hybridization” refers to the process in which twosingle-stranded polynucleotides bind non-covalently to form a stabledouble-stranded polynucleotide. The resulting (usually) double-strandedpolynucleotide is a “hybrid” or “duplex.” “Hybridization conditions”will typically include salt concentrations of less than about 1M, moreusually less than about 500 mM and may be less than about 200 mM. A“hybridization buffer” is a buffered salt solution such as 5% SSPE, orother such buffers known in the art. Hybridization temperatures can beas low as 5° C., but are typically greater than 22° C., and moretypically greater than about 30° C., and typically in excess of 37° C.Hybridizations are usually performed under stringent conditions, i.e.,conditions under which a probe will hybridize to its target subsequencebut will not hybridize to the other, uncomplimentary sequences.Stringent conditions are sequence-dependent and are different indifferent circumstances. For example, longer fragments may requirehigher hybridization temperatures for specific hybridization than shortfragments. As other factors may affect the stringency of hybridization,including base composition and length of the complementary strands,presence of organic solvents, and the extent of base mismatching, thecombination of parameters is more important than the absolute measure ofany one parameter alone. Generally stringent conditions are selected tobe about 5° C. lower than the T_(m) for the specific sequence at adefined ionic strength and pH. Exemplary stringent conditions include asalt concentration of at least 0.01M to no more than 1M sodium ionconcentration (or other salt) at a pH of about 7.0 to about 8.3 and atemperature of at least 25° C. For example, conditions of 5×SSPE (750 mMNaCl, 50 mM sodium phosphate, 5 mM EDTA at pH 7.4) and a temperature of30° C. are suitable for allele-specific probe hybridizations. Furtherexamples of stringent conditions are well known in the art, see forexample Sambrook J et al. (2001), Molecular Cloning, A LaboratoryManual, (3rd Ed., Cold Spring Harbor Laboratory Press.

As used herein, the term “T_(m)” generally refers to the temperature atwhich half of the population of double-stranded nucleic acid moleculesbecomes dissociated into single strands. The equation for calculatingthe Tm of nucleic acids is well known in the art. As indicated bystandard references, a simple estimate of the T_(m) value may becalculated by the equation:T_(m)=81.5+16.6(log10[Na+])0.41(%[G+C])−675/n−1.0 m, when a nucleic acidis in aqueous solution having cation concentrations of 0.5 M, or less,the (G+C) content is between 30% and 70%, n is the number of bases, andm is the percentage of base pair mismatches (see e.g., Sambrook J et al.(2001), Molecular Cloning, A Laboratory Manual, (3rd Ed., Cold SpringHarbor Laboratory Press). Other references include more sophisticatedcomputations, which take structural as well as sequence characteristicsinto account for the calculation of T_(m) (see also, Anderson and Young(1985), Quantitative Filter Hybridization, Nucleic Acid Hybridization,and Allawi and SantaLucia (1997), Biochemistry 36:10581-94).

In one example of a cPAL method, referred to herein as “single cPAL”, asillustrated in FIG. 23, anchor probe 2302 hybridizes to a complementaryregion on adaptor 2308 of the DNB 2301. Anchor probe 2302 hybridizes tothe adaptor region directly adjacent to target nucleic acid 2309, but insome cases, anchor probes can be designed to “reach into” the targetnucleic acid by incorporating a desired number of degenerate bases atthe terminus of the anchor probe, as is schematically illustrated inFIG. 24 and described further below. A pool of differentially labeledsequencing probes 2305 will hybridize to complementary regions of thetarget nucleic acid, and sequencing probes that hybridize adjacent toanchor probes are ligated to form a probe ligation product, usually byapplication of a ligase. The sequencing probes are generally sets orpools of oligonucleotides comprising two parts: different nucleotides atthe interrogation position, and then all possible bases (or a universalbase) at the other positions; thus, each probe represents each base typeat a specific position. The sequencing probes are labeled with adetectable label that differentiates each sequencing probe from thesequencing probes with other nucleotides at that position. Thus, in theexample illustrated in FIG. 23, a sequencing probe 2310 that hybridizesadjacent to anchor probe 2302 and is ligated to the anchor probe willidentify the base at a position in the target nucleic acid 5 bases fromthe adaptor as a “G”. FIG. 23 depicts a situation where theinterrogation base is 5 bases in from the ligation site, but as morefully described below, the interrogation base can also be “closer” tothe ligation site, and in some cases at the point of ligation. Onceligated, non-ligated anchor and sequencing probes are washed away, andthe presence of the ligation product on the array is detected using thelabel. Multiple cycles of anchor probe and sequencing probehybridization and ligation can be used to identify a desired number ofbases of the target nucleic acid on each side of each adaptor in a DNB.Hybridization of the anchor probe and the sequencing probe may occursequentially or simultaneously. The fidelity of the base call relies inpart on the fidelity of the ligase, which generally will not ligate ifthere is a mismatch close to the ligation site.

The present invention also provides methods in which two or more anchorprobes are used in every hybridization-ligation cycle. FIG. 25illustrate an additional example of a “double cPAL with overhang” methodin which a first anchor probe 2502 and a second anchor probe 2505 eachhybridize to complimentary regions of an adaptor. In the exampleillustrated in FIG. 25, the first anchor probe 2502 is fullycomplementary to a first region of the adaptor 2511, and the secondanchor probe 2505 is complementary to a second adaptor region adjacentto the hybridization position of the first anchor probe. The secondanchor probe also comprises degenerate bases at the terminus that is notadjacent to the first anchor probe. As a result, the second anchor probeis able to hybridize to a region of the target nucleic acid 2512adjacent to adaptor 2511 (the “overhang” portion). The second anchorprobe is generally too short to be maintained alone in its duplexhybridization state, but upon ligation to the first anchor probe itforms a longer anchor probe that is stably hybridized for subsequentmethods. As discussed above for the “single cPAL” method, a pool ofsequencing probes 2508 that represents each base type at a detectionposition of the target nucleic acid and labeled with a detectable labelthat differentiates each sequencing probe from the sequencing probeswith other nucleotides at that position is hybridized 2509 to theadaptor-anchor probe duplex and ligated to the terminal 5′ or 3′ base ofthe ligated anchor probes. In the example illustrated in FIG. 25, thesequencing probes are designed to interrogate the base that is fivepositions 5′ of the ligation point between the sequencing probe 2514 andthe ligated anchor probes 2513. Since the second adaptor probe 2505 hasfive degenerate bases at its 5′ end, it reaches five bases into thetarget nucleic acid 2512, allowing interrogation with the sequencingprobe at a full ten bases from the interface between the target nucleicacid 2512 and the adaptor 2511.

In variations of the above described examples of a double cPAL method,if the first anchor probe terminates closer to the end of the adaptor,the second adaptor probe will be proportionately more degenerate andtherefore will have a greater potential to not only ligate to the end ofthe first adaptor probe but also to ligate to other second adaptorprobes at multiple sites on the DNB. To prevent such ligation artifacts,the second anchor probes can be selectively activated to engage inligation to a first anchor probe or to a sequencing probe. Suchactivation methods are described in further detail below, and includemethods such as selectively modifying the termini of the anchor probessuch that they are able to ligate only to a particular anchor probe orsequencing probe in a particular orientation with respect to theadaptor.

Similar to the double cPAL method described above, it will beappreciated that cPAL methods utilizing three or more anchor probes arealso encompassed by the present invention.

In addition, sequencing reactions can be done at one or both of thetermini of each adaptor, e.g., the sequencing reactions can be“unidirectional” with detection occurring 3′ or 5′ of the adaptor or theother or the reactions can be “bidirectional” in which bases aredetected at detection positions 3′ and 5′ of the adaptor. Bidirectionalsequencing reactions can occur simultaneously—i.e., bases on both sidesof the adaptor are detected at the same time—or sequentially in anyorder.

Multiple cycles of cPAL (whether single, double, triple, etc.) willidentify multiple bases in the regions of the target nucleic acidadjacent to the adaptors. In brief, the cPAL methods are repeated forinterrogation of multiple adjacent bases within a target nucleic acid bycycling anchor probe hybridization and enzymatic ligation reactions withsequencing probe pools designed to detect nucleotides at varyingpositions removed from the interface between the adaptor and targetnucleic acid. In any given cycle, the sequencing probes used aredesigned such that the identity of one or more of bases at one or morepositions is correlated with the identity of the label attached to thatsequencing probe. Once the ligated sequencing probe (and hence thebase(s) at the interrogation position(s) is detected, the ligatedcomplex is stripped off of the DNB and a new cycle of adaptor andsequencing probe hybridization and ligation is conducted.

As will be appreciated, DNBs of the invention can be used in othersequencing methods in addition to the cPAL methods described above,including other sequencing by ligation methods as well as othersequencing methods, including without limitation sequencing byhybridization, sequencing by synthesis (including sequencing by primerextension), chained sequencing by ligation of cleavable probes, and thelike.

Methods similar to those described above for sequencing can also be usedto detect specific sequences in a target nucleic acid, includingdetection of single nucleotide polymorphisms (SNPs). In such methods,sequencing probes that will hybridize to a particular sequence, such asa sequence containing a SNP, will be applied. Such sequencing probes canbe differentially labeled to identify which SNP is present in the targetnucleic acid. Anchor probes can also be used in combination with suchsequencing probes to provide further stability and specificity.

VIIB. Sequencing

In one aspect, the present invention provides methods for identifyingsequences of DNBs by utilizing sequencing by ligation methods. In oneaspect, the present invention provides methods for identifying sequencesof DNBs that utilize a combinatorial probe anchor ligation (cPAL)method. Generally, cPAL involves identifying a nucleotide at a detectionposition in a target nucleic acid by detecting a probe ligation productformed by ligation of an anchor probe and a sequencing probe. Methods ofthe invention can be used to sequence a portion or the entire sequenceof the target nucleic acid contained in a DNB, and many DNBs thatrepresent a portion or all of a genome.

As discussed further herein, every DNB comprises repeating monomericunits, each monomeric unit comprising one or more adaptors and a targetnucleic acid. The target nucleic acid comprises a plurality of detectionpositions. The term “detection position” refers to a position in atarget sequence for which sequence information is desired. As will beappreciated by those in the art, generally a target sequence hasmultiple detection positions for which sequence information is required,for example in the sequencing of complete genomes as described herein.In some cases, for example in SNP analysis, it may be desirable to justread a single SNP in a particular area.

The present invention provides methods of sequencing that utilize acombination of anchor probes and sequencing probes. By “sequencingprobe” as used herein is meant an oligonucleotide that is designed toprovide the identity of a nucleotide at a particular detection positionof a target nucleic acid. Sequencing probes hybridize to domains withintarget sequences, e.g. a first sequencing probe may hybridize to a firsttarget domain, and a second sequencing probe may hybridize to a secondtarget domain. The terms “first target domain” and “second targetdomain” or grammatical equivalents herein means two portions of a targetsequence within a nucleic acid which is under examination. The firsttarget domain may be directly adjacent to the second target domain, orthe first and second target domains may be separated by an interveningsequence, for example an adaptor. The terms “first” and “second” are notmeant to confer an orientation of the sequences with respect to the5′-3′ orientation of the target sequence. For example, assuming a 5′-3′orientation of the complementary target sequence, the first targetdomain may be located either 5′ to the second domain, or 3′ to thesecond domain. Sequencing probes can overlap, e.g. a first sequencingprobe can hybridize to the first 6 bases adjacent to one terminus of anadaptor, and a second sequencing probe can hybrdize to the 4rd-9th basesfrom the terminus of the adaptor (for example when an anchor probe hasthree degenerate bases). Alternatively, a first sequencing probe canhybridize to the 6 bases adjacent to the “upstream” terminus of anadaptor and a second sequencing probe can hybridize to the 6 basesadjacent to the “downstream” terminus of an adaptor.

Sequencing probes will generally comprise a number of degenerate basesand a specific nucleotide at a specific location within the probe toquery the detection position (also referred to herein as an“interrogation position”).

In general, pools of sequencing probes are used when degenerate basesare used. That is, a probe having the sequence “NNNANN” is actually aset of probes of having all possible combinations of the four nucleotidebases at five positions (i.e., 1024 sequences) with an adenosine at the6th position. (As noted herein, this terminology is also applicable toadaptor probes: for example, when an adaptor probe has “three degeneratebases”, for example, it is actually a set of adaptor probes comprisingthe sequence corresponding to the anchor site, and all possiblecombinations at 3 positions, so it is a pool of 64 probes).

In some embodiments, for each interrogation position, four differentlylabeled pools can be combined in a single pool and used in a sequencingstep. Thus, in any particular sequencing step, 4 pools are used, eachwith a different specific base at the interrogation position and with adifferent label corresponding to the base at the interrogation position.That is, sequencing probes are also generally labeled such that aparticular nucleotide at a particular interrogation position isassociated with a label that is different from the labels of sequencingprobes with a different nucleotide at the same interrogation position.For example, four pools can be used: NNNANN-dye1, NNNTNN-dye2,NNNCNN-dye3 and NNNGNN-dye4 in a single step, as long as the dyes areoptically resolvable. In some embodiments, for example for SNPdetection, it may only be necessary to include two pools, as the SNPcall will be either a C or an A, etc. Similarly, some SNPs have threepossibilities. Alternatively, in some embodiments, if the reactions aredone sequentially rather than simultaneously, the same dye can be done,just in different steps: e.g. the NNNANN-dye1 probe can be used alone ina reaction, and either a signal is detected or not, and the probeswashed away; then a second pool, NNNTNN-dye1 can be introduced.

In any of the sequencing methods described herein, sequencing probes mayhave a wide range of lengths, including about 3 to about 25 bases. Infurther embodiments, sequencing probes may have lengths in the range ofabout 5 to about 20, about 6 to about 18, about 7 to about 16, about 8to about 14, about 9 to about 12, and about 10 to about 11 bases.

Sequencing probes of the present invention are designed to becomplementary, and in general, perfectly complementary, to a sequence ofthe target sequence such that hybridization of a portion target sequenceand probes of the present invention occurs. In particular, it isimportant that the interrogation position base and the detectionposition base be perfectly complementary and that the methods of theinvention do not result in signals unless this is true.

In many embodiments, sequencing probes are perfectly complementary tothe target sequence to which they hybridize; that is, the experimentsare run under conditions that favor the formation of perfectbasepairing, as is known in the art. As will be appreciated by those inthe art, a sequencing probe that is perfectly complementary to a firstdomain of the target sequence could be only substantially complementaryto a second domain of the same target sequence; that is, the presentinvention relies in many cases on the use of sets of probes, forexample, sets of hexamers, that will be perfectly complementary to sometarget sequences and not to others.

In some embodiments, depending on the application, the complementaritybetween the sequencing probe and the target need not be perfect; theremay be any number of base pair mismatches, which will interfere withhybridization between the target sequence and the single strandednucleic acids of the present invention. However, if the number ofmismatches is so great that no hybridization can occur under even theleast stringent of hybridization conditions, the sequence is not acomplementary target sequence. Thus, by “substantially complementary”herein is meant that the sequencing probes are sufficientlycomplementary to the target sequences to hybridize under normal reactionconditions. However, for most applications, the conditions are set tofavor probe hybridization only if perfectly complementarity exists.Alternatively, sufficient complementarity is required to allow theligase reaction to occur; that is, there may be mismatches in some partof the sequence but the interrogation position base should allowligation only if perfect complementarity at that position occurs.

In some cases, in addition to or instead of using degenerate bases inprobes of the invention, universal bases which hybridize to more thanone base can be used. For example, inosine can be used. Any combinationof these systems and probe components can be utilized.

Sequencing probes of use in methods of the present invention are usuallydetectably labeled. By “label” or “labeled” herein is meant that acompound has at least one element, isotope or chemical compound attachedto enable the detection of the compound. In general, labels of use inthe invention include without limitation isotopic labels, which may beradioactive or heavy isotopes, magnetic labels, electrical labels,thermal labels, colored and luminescent dyes, enzymes and magneticparticles as well. Dyes of use in the invention may be chromophores,phosphors or fluorescent dyes, which due to their strong signals providea good signal-to-noise ratio for decoding. Sequencing probes may also belabeled with quantum dots, fluorescent nanobeads or other constructsthat comprise more than one molecule of the same fluorophore. Labelscomprising multiple molecules of the same fluorophore will generallyprovide a stronger signal and will be less sensitive to quenching thanlabels comprising a single molecule of a fluorophore. It will beunderstood that any discussion herein of a label comprising afluorophore will apply to labels comprising single and multiplefluorophore molecules.

Many embodiments of the invention include the use of fluorescent labels.Suitable dyes for use in the invention include, but are not limited to,fluorescent lanthanide complexes, including those of Europium andTerbium, fluorescein, rhodamine, tetramethylrhodamine, eosin,erythrosin, coumarin, methyl-coumarins, pyrene, Malacite green,stilbene, Lucifer Yellow, Cascade Blue™, Texas Red, and others describedin the 6th Edition of the Molecular Probes Handbook by Richard P.Haugland, hereby expressly incorporated by reference in its entirety forall purposes and in particular for its teachings regarding labels of usein accordance with the present invention. Commercially availablefluorescent dyes for use with any nucleotide for incorporation intonucleic acids include, but are not limited to: Cy3, Cy5, (AmershamBiosciences, Piscataway, N.J., USA), fluorescein, tetramethylrhodamine-,Texas Red®, Cascade Blue®, BODIPY® FL-14, BODIPY®R, BODIPY® TR-14,Rhodamine Green™, Oregon Green® 488, BODIPY® 630/650, BODIPY® 650/665-,Alexa Fluor® 488, Alexa Fluor® 532, Alexa Fluor® 568, Alexa Fluor® 594,Alexa Fluor® 546 (Molecular Probes, Inc. Eugene, Oreg., USA), Quasar570, Quasar 670, Cal Red 610 (BioSearch Technologies, Novato, Calif.).Other fluorophores available for post-synthetic attachment include,inter alia, Alexa Fluor® 350, Alexa Fluor® 532, Alexa Fluor® 546, AlexaFluor® 568, Alexa Fluor® 594, Alexa Fluor® 647, BODIPY 493/503, BODIPYFL, BODIPY R6G, BODIPY 530/550, BODIPY TMR, BODIPY 558/568, BODIPY558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY 630/650,BODIPY 650/665, Cascade Blue, Cascade Yellow, Dansyl, lissaminerhodamine B, Marina Blue, Oregon Green 488, Oregon Green 514, PacificBlue, rhodamine 6G, rhodamine green, rhodamine red,tetramethylrhodamine, Texas Red (available from Molecular Probes, Inc.,Eugene, Oreg., USA), and Cy2, Cy3.5, Cy5.5, and Cy7 (AmershamBiosciences, Piscataway, N.J. USA, and others). In some embodiments, thelabels used include fluoroscein, Cy3, Texas Red, Cy5, Quasar 570, Quasar670 and Cal Red 610 are used in methods of the present invention.

Labels can be attached to nucleic acids to form the labeled sequencingprobes of the present invention using methods known in the art, and to avariety of locations of the nucleosides. For example, attachment can beat either or both termini of the nucleic acid, or at an internalposition, or both. For example, attachment of the label may be done on aribose of the ribose-phosphate backbone at the 2′ or 3′ position (thelatter for use with terminal labeling), in one embodiment through anamide or amine linkage. Attachment may also be made via a phosphate ofthe ribose-phosphate backbone, or to the base of a nucleotide. Labelscan be attached to one or both ends of a probe or to any one of thenucleotides along the length of a probe.

Sequencing probes are structured differently depending on theinterrogation position desired. For example, in the case of sequencingprobes labeled with fluorophores, a single position within eachsequencing probe will be correlated with the identity of the fluorophorewith which it is labeled. Generally, the fluorophore molecule will beattached to the end of the sequencing probe that is opposite to the endtargeted for ligation to the anchor probe.

By “anchor probe” as used herein is meant an oligonucleotide designed tobe complementary to at least a portion of an adaptor, referred to hereinas “an anchor site”. Adaptors can contain multiple anchor sites forhybridization with multiple anchor probes, as described herein. Asdiscussed further herein, anchor probes of use in the present inventioncan be designed to hybridize to an adaptor such that at least one end ofthe anchor probe is flush with one terminus of the adaptor (either“upstream” or “downstream”, or both). In further embodiments, anchorprobes can be designed to hybridize to at least a portion of an adaptor(a first adaptor site) and also at least one nucleotide of the targetnucleic acid adjacent to the adaptor (“overhangs”). As illustrated inFIG. 24, anchor probe 2402 comprises a sequence complementary to aportion of the adaptor. Anchor probe 2402 also comprises four degeneratebases at one terminus. This degeneracy allows for a portion of theanchor probe population to fully or partially match the sequence of thetarget nucleic acid adjacent to the adaptor and allows the anchor probeto hybridize to the adaptor and reach into the target nucleic acidadjacent to the adaptor regardless of the identity of the nucleotides ofthe target nucleic acid adjacent to the adaptor. This shift of theterminal base of the anchor probe into the target nucleic acid shiftsthe position of the base to be called closer to the ligation point, thusallowing the fidelity of the ligase to be maintained. In general,ligases ligate probes with higher efficiency if the probes are perfectlycomplementary to the regions of the target nucleic acid to which theyare hybridized, but the fidelity of ligases decreases with distance awayfrom the ligation point. Thus, in order to minimize and/or preventerrors due to incorrect pairing between a sequencing probe and thetarget nucleic acid, it can be useful to maintain the distance betweenthe nucleotide to be detected and the ligation point of the sequencingand anchor probes. By designing the anchor probe to reach into thetarget nucleic acid, the fidelity of the ligase is maintained whilestill allowing a greater number of nucleotides adjacent to each adaptorto be identified. Although the embodiment illustrated in FIG. 24 is onein which the sequencing probe hybridizes to a region of the targetnucleic acid on one side of the adaptor, it will be appreciated thatembodiments in which the sequencing probe hybridizes on the other sideof the adaptor are also encompassed by the invention. In FIG. 24, “N”represents a degenerate base and “B” represents nucleotides ofundetermined sequence. As will be appreciated, in some embodiments,rather than degenerate bases, universal bases may be used.

Anchor probes of the invention may comprise any sequence that allows theanchor probe to hybridize to a DNB, generally to an adaptor of a DNB.Such anchor probes may comprise a sequence such that when the anchorprobe is hybridized to an adaptor, the entire length of the anchor probeis contained within the adaptor. In some embodiments, anchor probes maycomprise a sequence that is complementary to at least a portion of anadaptor and also comprise degenerate bases that are able to hybridize totarget nucleic acid regions adjacent to the adaptor. In some exemplaryembodiments, anchor probes are hexamers that comprise 3 bases that arecomplementary to an adaptor and 3 degenerate bases. In some exemplaryembodiments, anchor probes are 8-mers that comprise 3 bases that arecomplementary to an adaptor and 5 degenerate bases. In further exemplaryembodiments, particularly when multiple anchor probes are used, a firstanchor probe comprises a number of bases complementary to an adaptor atone end and degenerate bases at another end, whereas a second anchorprobe comprises all degenerate bases and is designed to ligate to theend of the first anchor probe that comprises degenerate bases. It willbe appreciated that these are exemplary embodiments, and that a widerange of combinations of known and degenerate bases can be used toproduce anchor probes of use in accordance with the present invention.

The present invention provides sequencing by ligation methods foridentifying sequences of DNBs. In certain aspects, the sequencing byligation methods of the invention include providing differentcombinations of anchor probes and sequencing probes, which, whenhybridized to adjacent regions on a DNB, can be ligated to form probeligation products. The probe ligation products are then detected, whichprovides the identity of one or more nucleotides in the target nucleicacid. By “ligation” as used herein is meant any method of joining two ormore nucleotides to each other. Ligation can include chemical as well asenzymatic ligation. In general, the sequencing by ligation methodsdiscussed herein utilize enzymatic ligation by ligases. Such ligasesinvention can be the same or different than ligases discussed above forcreation of the nucleic acid templates. Such ligases include withoutlimitation DNA ligase I, DNA ligase II, DNA ligase III, DNA ligase IV,E. coli DNA ligase, T4 DNA ligase, T4 RNA ligase 1, T4 RNA ligase 2, T7ligase, T3 DNA ligase, and thermostable ligases (including withoutlimitation Taq ligase) and the like. As discussed above, sequencing byligation methods often rely on the fidelity of ligases to only joinprobes that are perfectly complementary to the nucleic acid to whichthey are hybridized. This fidelity will decrease with increasingdistance between a base at a particular position in a probe and theligation point between the two probes. As such, conventional sequencingby ligation methods can be limited in the number of bases that can beidentified. The present invention increases the number of bases that canbe identified by using multiple probe pools, as is described furtherherein.

A variety of hybridization conditions may be used in the sequencing byligation methods of sequencing as well as other methods of sequencingdescribed herein. These conditions include high, moderate and lowstringency conditions; see for example Maniatis et al., MolecularCloning: A Laboratory Manual, 2d Edition, 1989, and Short Protocols inMolecular Biology, ed. Ausubel, et al, which are hereby incorporated byreference. Stringent conditions are sequence-dependent and will bedifferent in different circumstances. Longer sequences hybridizespecifically at higher temperatures. An extensive guide to thehybridization of nucleic acids is found in Tijssen, Techniques inBiochemistry and Molecular Biology—Hybridization with Nucleic AcidProbes, “Overview of principles of hybridization and the strategy ofnucleic acid assays,” (1993). Generally, stringent conditions areselected to be about 5-10° C. lower than the thermal melting point (Tm)for the specific sequence at a defined ionic strength and pH. The Tm isthe temperature (under defined ionic strength, pH and nucleic acidconcentration) at which 50% of the probes complementary to the targethybridize to the target sequence at equilibrium (as the target sequencesare present in excess, at Tm, 50% of the probes are occupied atequilibrium). Stringent conditions can be those in which the saltconcentration is less than about 1.0 M sodium ion, typically about 0.01to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 andthe temperature is at least about 30° C. for short probes (e.g. 10 to 50nucleotides) and at least about 60° C. for long probes (e.g. greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of helix destabilizing agents such as formamide. Thehybridization conditions may also vary when a non-ionic backbone, i.e.PNA is used, as is known in the art. In addition, cross-linking agentsmay be added after target binding to cross-link, i.e. covalently attach,the two strands of the hybridization complex.

Although much of the description of sequencing methods is provided interms of nucleic acid templates of the invention, it will be appreciatedthat these sequencing methods also encompass identifying sequences inDNBs generated from such nucleic acid templates, as described herein.

For any of sequencing methods known in the art and described hereinusing nucleic acid templates of the invention, the present inventionprovides methods for determining at least about 10 to about 200 bases intarget nucleic acids. In further embodiments, the present inventionprovides methods for determining at least about 20 to about 180, about30 to about 160, about 40 to about 140, about 50 to about 120, about 60to about 100, and about 70 to about 80 bases in target nucleic acids. Instill further embodiments, sequencing methods are used to identify atleast 5, 10, 15, 20, 25, 30 or more bases adjacent to one or both endsof each adaptor in a nucleic acid template of the invention.

Any of the sequencing methods described herein and known in the art canbe applied to nucleic acid templates and/or DNBs of the invention insolution or to nucleic acid templates and/or DNBs disposed on a surfaceand/or in an array.

VIIB(i). Single cPAL

In one aspect, the present invention provides methods for identifyingsequences of DNBs by using combinations of sequencing and anchor probesthat hybridize to adjacent regions of a DNB and are ligated, usually byapplication of a ligase. Such methods are generally referred to hereinas cPAL (combinatorial probe anchor ligation) methods. In one aspect,cPAL methods of the invention produce probe ligation products comprisinga single anchor probe and a single sequencing probe. Such cPAL methodsin which only a single anchor probe is used are referred to herein as“single cPAL”.

One embodiment of single cPAL is illustrated in FIG. 23. A monomericunit 2301 of a DNB comprises a target nucleic acid 2309 and an adaptor2308. An anchor probe 2302 hybridizes to a complementary region onadaptor 2308. In the example illustrated in FIG. 23, anchor probe 2302hybridizes to the adaptor region directly adjacent to target nucleicacid 2309, although, as is discussed further herein, anchor probes canalso be designed to reach into the target nucleic acid adjacent to anadaptor by incorporating a desired number of degenerate bases at theterminus of the anchor probe. A pool of differentially labeledsequencing probes 2306 will hybridize to complementary regions of thetarget nucleic acid. A sequencing probe 2310 that hybridizes to theregion of target nucleic acid 2309 adjacent to anchor probe 2302 will beligated to the anchor probe form a probe ligation product. Theefficiency of hybridization and ligation is increased when the base inthe interrogation position of the probe is complementary to the unknownbase in the detection position of the target nucleic acid. Thisincreased efficiency favors ligation of perfectly complementarysequencing probes to anchor probes over mismatch sequencing probes. Asdiscussed above, ligation is generally accomplished enzymatically usinga ligase, but other ligation methods can also be utilized in accordancewith the invention. In FIG. 23, “N” represents a degenerate base and “B”represents nucleotides of undetermined sequence. As will be appreciated,in some embodiments, rather than degenerate bases, universal bases maybe used.

As also discussed above, the sequencing probes can be oligonucleotidesrepresenting each base type at a specific position and labeled with adetectable label that differentiates each sequencing probe from thesequencing probes with other nucleotides at that position. Thus, in theexample illustrated in FIG. 23, a sequencing probe 2310 that hybridizesadjacent to anchor probe 2302 and is ligated to the anchor probe willidentify the base at a position in the target nucleic acid 5 bases fromthe adaptor as a “G”. Multiple cycles of anchor probe and sequencingprobe hybridization and ligation can be used to identify a desirednumber of bases of the target nucleic acid on each side of each adaptorin a DNB.

As will be appreciated, hybridization of the anchor probe and thesequencing probe can be sequential or simultaneous in any of the cPALmethods described herein.

In the embodiment illustrated in FIG. 23, sequencing probe 2310hybridizes to a region “upstream” of the adaptor, however it will beappreciated that sequencing probes may also hybridize “downstream” ofthe adaptor. The terms “upstream” and “downstream” refer to the regions5′ and 3′ of the adaptor, depending on the orientation of the system. Ingeneral, “upstream” and “downstream” are relative terms and are notmeant to be limiting; rather they are used for ease of understanding. Asillustrated in FIG. 6, a sequencing probe 607 can hybridize downstreamof adaptor 604 to identify a nucleotide 4 bases away from the interfacebetween the adaptor and the target nucleic acid 603. In furtherembodiments, sequencing probes can hybridize both upstream anddownstream of the adaptor to identify nucleotides at positions in thenucleic acid on both sides of the adaptor. Such embodiments allowgeneration of multiple points of data from each adaptor for eachhybridization-ligation-detection cycle of the single cPAL method.

In some embodiments, probes used in a single cPAL method may have fromabout 3 to about 20 bases corresponding to an adaptor and from about 1to about 20 degenerate bases (i.e., in a pool of anchor probes). Suchanchor probes may also include universal bases, as well as combinationsof degenerate and universal bases.

In some embodiments, anchor probes with degenerated bases may have about1-5 mismatches with respect to the adaptor sequence to increase thestability of full match hybridization at the degenerated bases. Such adesign provides an additional way to control the stability of theligated anchor and sequencing probes to favor those probes that areperfectly matched to the target (unknown) sequence. In furtherembodiments, a number of bases in the degenerate portion of the anchorprobes may be replaced with abasic sites (i.e., sites which do not havea base on the sugar) or other nucleotide analogs to influence thestability of the hybridized probe to favor the full match hybrid at thedistal end of the degenerate part of the anchor probe that willparticipate in the ligation reactions with the sequencing probes, asdescribed herein. Such modifications may be incorporated, for example,at interior bases, particularly for anchor probes that comprise a largenumber (i.e., greater than 5) of degenerated bases. In addition, some ofthe degenerated or universal bases at the distal end of the anchor probemay be designed to be cleavable after hybridization (for example byincorporation of a uracil) to generate a ligation site to the sequencingprobe or to a second anchor probe, as described further below.

In further embodiments, the hybridization of the anchor probes can becontrolled through manipulation of the reaction conditions, for examplethe stringency of hybridization. In an exemplary embodiment, the anchorhybridization process may start with conditions of high stringency(higher temperature, lower salt, higher pH, higher concentration offormamide, and the like), and these conditions may be gradually orstepwise relaxed. This may require consecutive hybridization cycles inwhich different pools of anchor probes are removed and then added insubsequent cycles. Such methods provide a higher percentage of targetnucleic acid occupied with perfectly complementary anchor probes,particularly anchor probes perfectly complementary at positions at thedistal end that will be ligated to the sequencing probe. Hybridizationtime at each stringency condition may also be controlled to obtaingreater numbers of full match hybrids.

VIIB(ii). Double cPAL (and Beyond)

In still further embodiments, the present invention provides cPALmethods utilizing two ligated anchor probes in everyhybridization-ligation cycle. See for example U.S. Patent ApplicationSer. Nos. 60/992,485; 61/026,337; 61/035,914 and 61/061,134, which arehereby expressly incorporated by reference in their entirety, andespecially the examples and claims. FIG. 25 illustrates an example of a“double cPAL” method in which a first anchor probe 2502 and a secondanchor probe 2505 hybridize to complimentary regions of an adaptor; thatis, the first anchor probe hybridizes to the first anchor site and thesecond anchor probe hybridizes to the second adaptor site. In theexample illustrated in FIG. 25, the first anchor probe 2502 is fullycomplementary to a region of the adaptor 2511 (the first anchor site),and the second anchor probe 2505 is complementary to the adaptor regionadjacent to the hybridization position of the first anchor probe (thesecond anchor site). In general, the first and second anchor sites areadjacent.

The second anchor probe may optionally also comprises degenerate basesat the terminus that is not adjacent to the first anchor probe such thatit will hybridize to a region of the target nucleic acid 2512 adjacentto adaptor 2511. This allows sequence information to be generated fortarget nucleic acid bases farther away from the adaptor/targetinterface. Again, as outlined herein, when a probe is said to have“degenerate bases”, it means that the probe actually comprises a set ofprobes, with all possible combinations of sequences at the degeneratepositions. For example, if an anchor probe is 9 bases long with 6 knownbases and three degenerate bases, the anchor probe is actually a pool of64 probes.

The second anchor probe is generally too short to be maintained alone inits duplex hybridization state, but upon ligation to the first anchorprobe it forms a longer anchor probe that is stable for subsequentmethods. In the some embodiments, the second anchor probe has about 1 toabout 5 bases that are complementary to the adaptor and about 5 to about10 bases of degenerate sequence. As discussed above for the “singlecPAL” method, a pool of sequencing probes 2508 representing each basetype at a detection position of the target nucleic acid and labeled witha detectable label that differentiates each sequencing probe from thesequencing probes with other nucleotides at that position is hybridized2509 to the adaptor-anchor probe duplex and ligated to the terminal 5′or 3′ base of the ligated anchor probes. In the example illustrated inFIG. 25, the sequencing probes are designed to interrogate the base thatis five positions 5′ of the ligation point between the sequencing probe2514 and the ligated anchor probes 2513. Since the second anchor probe2505 has five degenerate bases at its 5′ end, it reaches 5 bases intothe target nucleic acid 2512, allowing interrogation with the sequencingprobe at a full 10 bases from the interface between the target nucleicacid 2512 and the adaptor 2511. In FIG. 25, “N” represents a degeneratebase and “B” represents nucleotides of undetermined sequence. As will beappreciated, in some embodiments, rather than degenerate bases,universal bases may be used.

In some embodiments, the second anchor probe may have about 5-10 basescorresponding to an adaptor and about 5-15 bases, which are generallydegenerated, corresponding to the target nucleic acid. This secondanchor probe may be hybridized first under optimal conditions to favorhigh percentages of target occupied with full match at a few basesaround the ligation point between the two anchor probes. The firstadaptor probe and/or the sequencing probe may be hybridized and ligatedto the second anchor probe in a single step or sequentially. In someembodiments, the first and second anchor probes may have at theirligation point from about 5 to about 50 complementary bases that are notcomplementary to the adaptor, thus forming a “branching-out” hybrid.This design allows an adaptor-specific stabilization of the hybridizedsecond anchor probe. In some embodiments, the second anchor probe isligated to the sequencing probe before hybridization of the first anchorprobe; in some embodiments the second anchor probe is ligated to thefirst anchor probe prior to hybridization of the sequencing probe; insome embodiments the first and second anchor probes and the sequencingprobe hybridize simultaneously and ligation occurs between the first andsecond anchor probe and between the second anchor probe and thesequencing probe simultaneously or essentially simultaneously, while inother embodiments the ligation between the first and second anchor probeand between the second anchor probe and the sequencing probe occurssequentially in any order. Stringent washing conditions can be used toremove unligated probes; (e.g., using temperature, pH, salt, a bufferwith an optimal concentration of formamide can all be used, with optimalconditions and/or concentrations being determined using methods known inthe art). Such methods can be particularly useful in methods utilizingsecond anchor probes with large numbers of degenerated bases that arehybridized outside of the corresponding junction point between theanchor probe and the target nucleic acid.

In certain embodiments, double cPAL methods utilize ligation of twoanchor probes in which one anchor probe is fully complementary to anadaptor and the second anchor probe is fully degenerate (again, actuallya pool of probes). An example of such a double cPAL method isillustrated in FIG. 26, in which the first anchor probe 2602 ishybridized to adaptor 2611 of DNB 2601. The second anchor probe 2605 isfully degenerate and is thus able to hybridize to the unknownnucleotides of the region of the target nucleic acid 2612 adjacent toadaptor 2611. The second anchor probe is designed to be too short to bemaintained alone in its duplex hybridization state, but upon ligation tothe first anchor probe the formation of the longer ligated anchor probeconstruct provides the stability needed for subsequent steps of the cPALprocess. The second fully degenerate anchor probe may in someembodiments be from about 5 to about 20 bases in length. For longerlengths (i.e., above 10 bases), alterations to hybridization andligation conditions may be introduced to lower the effective Tm of thedegenerate anchor probe. The shorter second anchor probe will generallybind non-specifically to target nucleic acid and adaptors, but itsshorter length will affect hybridization kinetics such that in generalonly those second anchor probes that are perfectly complementary toregions adjacent to the adaptors and the first anchor probes will havethe stability to allow the ligase to join the first and second anchorprobes, generating the longer ligated anchor probe construct.Non-specifically hybridized second anchor probes will not have thestability to remain hybridized to the DNB long enough to subsequently beligated to any adjacently hybridized sequencing probes. In someembodiments, after ligation of the second and first anchor probes, anyunligated anchor probes will be removed, usually by a wash step. In FIG.26, “N” represents a degenerate base and “B” represents nucleotides ofundetermined sequence. As will be appreciated, in some embodiments,rather than degenerate bases, universal bases may be used.

In further exemplary embodiments, the first anchor probe will be ahexamer comprising 3 bases complementary to the adaptor and 3 degeneratebases, whereas the second anchor probe comprises only degenerate basesand the first and second anchor probes are designed such that only theend of the first anchor probe with the degenerate bases will ligate tothe second anchor probe. In further exemplary embodiments, the firstanchor probe is an 8-mer comprising 3 bases complementary to an adaptorand 5 degenerate bases, and again the first and second anchor probes aredesigned such that only the end of the first anchor probe with thedegenerate bases will ligate to the second anchor probe. It will beappreciated that these are exemplary embodiments and that a wide rangeof combinations of known and degenerate bases can be used in the designof both the first and second (and in some embodiments the third and/orfourth) anchor probes.

In variations of the above described examples of a double cPAL method,if the first anchor probe terminates closer to the end of the adaptor,the second anchor probe will be proportionately more degenerate andtherefore will have a greater potential to not only ligate to the end ofthe first anchor probe but also to ligate to other second anchor probesat multiple sites on the DNB. To prevent such ligation artifacts, thesecond anchor probes can be selectively activated to engage in ligationto a first anchor probe or to a sequencing probe. Such activationinclude selectively modifying the termini of the anchor probes such thatthey are able to ligate only to a particular anchor probe or sequencingprobe in a particular orientation with respect to the adaptor. Forexample, 5′ and 3′ phosphate groups can be introduced to the secondanchor probe, with the result that the modified second anchor probewould be able to ligate to the 3′ end of a first anchor probe hybridizedto an adaptor, but two second anchor probes would not be able to ligateto each other (because the 3′ ends are phosphorylated, which wouldprevent enzymatic ligation). Once the first and second anchor probes areligated, the 3′ ends of the second anchor probe can be activated byremoving the 3′ phosphate group (for example with T4 polynucleotidekinase or phosphatases such as shrimp alkaline phosphatase and calfintestinal phosphatase).

If it is desired that ligation occur between the 3′ end of the secondanchor probe and the 5′ end of the first anchor probe, the first anchorprobe can be designed and/or modified to be phosphorylated on its 5′ endand the second anchor probe can be designed and/or modified to have no5′ or 3′ phosphorylation. Again, the second anchor probe would be ableto ligate to the first anchor probe, but not to other second anchorprobes. Following ligation of the first and second anchor probes, a 5′phosphate group can be produced on the free terminus of the secondanchor probe (for example, by using T4 polynucleotide kinase) to make itavailable for ligation to sequencing probes in subsequent steps of thecPAL process.

In some embodiments, the two anchor probes are applied to the DNBssimultaneously. In some embodiments, the two anchor probes are appliedto the DNBs sequentially, allowing one of the anchor probes to hybridizeto the DNBs before the other. In some embodiments, the two anchor probesare ligated to each other before the second adaptor is ligated to thesequencing probe. In some embodiments, the anchor probes and thesequencing probe are ligated in a single step. In embodiments in whichtwo anchor probes and the sequencing probe are ligated in a single step,the second adaptor can be designed to have enough stability to maintainits position until all three probes (the two anchor probes and thesequencing probe) are in place for ligation. For example, a secondanchor probe comprising five bases complementary to the adaptor and fivedegenerate bases for hybridization to the region of the target nucleicacid adjacent to the adaptor can be used. Such a second anchor probe mayhave sufficient stability to be maintained with low stringency washing,and thus a ligation step would not be necessary between the steps ofhybridization of the second anchor probe and hybridization of asequencing probe. In the subsequent ligation of the sequencing probe tothe second anchor probe, the second anchor probe would also be ligatedto the first anchor probe, resulting in a duplex with increasedstability over any of the anchor probes or sequencing probes alone.

Similar to the double cPAL method described above, it will beappreciated that cPAL with three or more anchor probes is alsoencompassed by the present invention. Such anchor probes can be designedin accordance with methods described herein and known in the art tohybridize to regions of adaptors such that one terminus of one of theanchor probes is available for ligation to sequencing probes hybridizedadjacent to the terminal anchor probe. In an exemplary embodiment, threeanchor probes are provided—two are complementary to different sequenceswithin an adaptor and the third comprises degenerate bases to hybridizeto sequences within the target nucleic acid. In a further embodiment,one of the two anchors complementary to sequences within the adaptor mayalso comprise one or more degenerate bases at on terminus, allowing thatanchor probe to reach into the target nucleic acid for ligation with thethird anchor probe. In further embodiments, one of the anchor probes maybe fully or partially complementary to the adaptor and the second andthird anchor probes will be fully degenerate for hybridization to thetarget nucleic acid. Four or more fully degenerate anchor probes can infurther embodiments be ligated sequentially to the three ligated anchorprobes to achieve extension of reads further into the target nucleicacid sequence. In an exemplary embodiment, a first anchor probecomprising twelve bases complementary to an adaptor may ligate with asecond hexameric anchor probe in which all six bases are degenerate. Athird anchor, also a fully degenerate hexamer, can also ligate to thesecond anchor probe to further extend into the unknown sequence of thetarget nucleic acid. A fourth, fifth, sixth, etc. anchor probe may alsobe added to extend even further into the unknown sequence. In stillfurther embodiments and in accordance with any of the cPAL methodsdescribed herein, one or more of the anchor probes may comprise one ormore labels that serve to “tag” the anchor probe and/or identify theparticular anchor probe hybridized to an adaptor of a DNB.

VIIB(iii). Detecting Fluorescently Labeled Sequencing Probes

As discussed above, sequencing probes used in accordance with thepresent invention may be detectably labeled with a wide variety oflabels. Although the following description is primarily directed toembodiments in which the sequencing probes are labeled withfluorophores, it will be appreciated that similar embodiments utilizingsequencing probes comprising other kinds of labels are encompassed bythe present invention.

Multiple cycles of cPAL (whether single, double, triple, etc.) willidentify multiple bases in the regions of the target nucleic acidadjacent to the adaptors. In brief, the cPAL methods are repeated forinterrogation of multiple bases within a target nucleic acid by cyclinganchor probe hybridization and enzymatic ligation reactions withsequencing probe pools designed to detect nucleotides at varyingpositions removed from the interface between the adaptor and targetnucleic acid. In any given cycle, the sequencing probes used aredesigned such that the identity of one or more of bases at one or morepositions is correlated with the identity of the label attached to thatsequencing probe. Once the ligated sequencing probe (and hence thebase(s) at the interrogation position(s) is detected, the ligatedcomplex is stripped off of the DNB and a new cycle of adaptor andsequencing probe hybridization and ligation is conducted.

In general, four fluorophores are generally used to identify a base atan interrogation position within a sequencing probe, and a single baseis queried per hybridization-ligation-detection cycle. However, as willbe appreciated, embodiments utilizing 8, 16, 20 and 24 fluorophores ormore are also encompassed by the present invention. Increasing thenumber of fluorophores increases the number of bases that can beidentified during any one cycle.

In one exemplary embodiment, a set of 7-mer pools of sequencing probesis employed having the following structures:

3′-Fl-NNNNNNAp 3′-F2-NNNNNNGp 3′-F3-NNNNNNCp 3′-F4-NNNNNNTp

The “p” represents a phosphate available for ligation and “N” representsdegenerate bases. F1-F4 represent four different fluorophores—eachfluorophore is thus associated with a particular base. This exemplaryset of probes would allow detection of the base immediately adjacent tothe adaptor upon ligation of the sequencing probe to an anchor probehybridized to the adaptor. To the extent that the ligase used to ligatethe sequencing probe to the anchor probe discriminates forcomplementarity between the base at the interrogation position of theprobe and the base at the detection position of the target nucleic acid,the fluorescent signal that would be detected upon hybridization andligation of the sequencing probe provides the identity of the base atthe detection position of the target nucleic acid.

In some embodiments, a set of sequencing probes will comprise threedifferentially labeled sequencing probes, with a fourth optionalsequencing probe left unlabeled.

After performing a hybridization-ligation-detection cycle, the anchorprobe-sequencing probe ligation products are stripped and a new cycle isbegun. In some embodiments, accurate sequence information can beobtained as far as six bases or more from the ligation point between theanchor and sequencing probes and as far as twelve bases or more from theinterface between the target nucleic acid and the adaptor. The number ofbases that can be identified can be increased using methods describedherein, including the use of anchor probes with degenerate ends that areable to reach further into the target nucleic acid.

Imaging acquisition may be performed using methods known in the art,including the use of commercial imaging packages such as Metamorph(Molecular Devices, Sunnyvale, Calif.). Data extraction may be performedby a series of binaries written in, e.g., C/C++ and base-calling andread-mapping may be performed by a series of Matlab and Perl scripts.

In an exemplary embodiment, DNBs disposed on a surface undergo a cycleof cPAL as described herein in which the sequencing probes utilized arelabeled with four different fluorophores (each corresponding to aparticular base at an interrogation position within the probe). Todetermine the identity of a base of each DNB disposed on the surface,each field of view (“frame”) is imaged with four different wavelengthscorresponding the to the four fluorescently labeled sequencing probes.All images from each cycle are saved in a cycle directory, where thenumber of images is four times the number of frames (when fourfluorophores are used). Cycle image data can then be saved into adirectory structure organized for downstream processing.

In some embodiments, data extraction will rely on two types of imagedata: bright-field images to demarcate the positions of all DNBs on asurface, and sets of fluorescence images acquired during each sequencingcycle. Data extraction software can be used to identify all objects withthe bright-field images and then for each such object, the software canbe used to compute an average fluorescence value for each sequencingcycle. For any given cycle, there are four data points, corresponding tothe four images taken at different wavelengths to query whether thatbase is an A, G, C or T. These raw data points (also referred to hereinas “base calls”) are consolidated, yielding a discontinuous sequencingread for each DNB.

The population of identified bases can then be assembled to providesequence information for the target nucleic acid and/or identify thepresence of particular sequences in the target nucleic acid. In someembodiments, the identified bases are assembled into a complete sequencethrough alignment of overlapping sequences obtained from multiplesequencing cycles performed on multiple DNBs. As used herein, the term“complete sequence” refers to the sequence of partial or whole genomesas well as partial or whole target nucleic acids. In furtherembodiments, assembly methods utilize algorithms that can be used to“piece together” overlapping sequences to provide a complete sequence.In still further embodiments, reference tables are used to assist inassembling the identified sequences into a complete sequence. Areference table may be compiled using existing sequencing data on theorganism of choice. For example human genome data can be accessedthrough the National Center for Biotechnology Information atftp.ncbi.nih.gov/refseq/release, or through the J. Craig VenterInstitute at http://www.jcvi.org/researchhuref/. All or a subset ofhuman genome information can be used to create a reference table forparticular sequencing queries. In addition, specific reference tablescan be constructed from empirical data derived from specificpopulations, including genetic sequence from humans with specificethnicities, geographic heritage, religious or culturally-definedpopulations, as the variation within the human genome may slant thereference data depending upon the origin of the information containedtherein.

In any of the embodiments of the invention discussed herein, apopulation of nucleic acid templates and/or DNBs may comprise a numberof target nucleic acids to substantially cover a whole genome or a wholetarget polynucleotide. As used herein, “substantially covers” means thatthe amount of nucleotides (i.e., target sequences) analyzed contains anequivalent of at least two copies of the target polynucleotide, or inanother aspect, at least ten copies, or in another aspect, at leasttwenty copies, or in another aspect, at least 100 copies. Targetpolynucleotides may include DNA fragments, including genomic DNAfragments and cDNA fragments, and RNA fragments. Guidance for the stepof reconstructing target polynucleotide sequences can be found in thefollowing references, which are incorporated by reference: Lander et al,Genomics, 2: 231-239 (1988); Vingron et al, J. Mol. Biol., 235: 1-12(1994); and like references.

VIIB(iv). Sets of Probes

As will be appreciated, different combinations of sequencing and anchorprobes can be used in accordance with the various cPAL methods describedabove. The following descriptions of sets of probes (also referred toherein as “pools of probes”) of use in the present invention areexemplary embodiments and it will be appreciated that the presentinvention is not limited to these combinations.

In one aspect, sets of probes are designed for identification ofnucleotides at positions at a specific distance from an adaptor. Forexample, certain sets of probes can be used to identify bases up to 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30 and more positions away from the adaptor.As discussed above, anchor probes with degenerate bases at one terminuscan be designed to reach into the target nucleic acid adjacent to anadaptor, allowing sequencing probes to ligate further away from theadaptor and thus provide the identity of a base further away from theadaptor.

In an exemplary embodiment, a set of probes comprises at least twoanchor probes designed to hybridize to adjacent regions of an adaptor.In one embodiment, the first anchor probe is fully complementary to aregion of the adaptor, while the second anchor probe is complementary tothe adjacent region of the adaptor. In some embodiments, the secondanchor probe will comprise one or more degenerate nucleotides thatextend into and hybridize to nucleotides of the target nucleic acidadjacent to the adaptor. In an exemplary embodiment, the second anchorprobe comprises at least 1-10 degenerate bases. In a further exemplaryembodiment, the second anchor probe comprises 2-9, 3-8, 4-7, and 5-6degenerate bases. In a still further exemplary embodiment, the secondanchor probe comprises one or more degenerate bases at one or bothtermini and/or within an interior region of its sequence.

In a further embodiment, a set of probes will also comprise one or moregroups of sequencing probes for base determination in one or moredetection positions with a target nucleic acid. In one embodiment, theset comprises enough different groups of sequencing probes to identifyabout 1 to about 20 positions within a target nucleic acid. In a furtherexemplary embodiment, the set comprises enough groups of sequencingprobes to identify about 2 to about 18, about 3 to about 16, about 4 toabout 14, about 5 to about 12, about 6 to about 10, and about 7 to about8 positions within a target nucleic acid.

In further exemplary embodiments, 10 pools of labeled or tagged probeswill be used in accordance with the invention. In still furtherembodiments, sets of probes will include two or more anchor probes withdifferent sequences. In yet further embodiments, sets of probes willinclude 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more anchorprobes with different sequences.

In a further exemplary embodiment, a set of probes is providedcomprising one or more groups of sequencing probes and three anchorprobes. The first anchor probe is complementary to a first region of anadaptor, the second anchor probe is complementary to a second region ofan adaptor, and the second region and the first region are adjacent toeach other. The third anchor probe comprises three or more degeneratenucleotides and is able to hybridize to nucleotides in the targetnucleic acid adjacent to the adaptor. The third anchor probe may also insome embodiments be complementary to a third region of the adaptor, andthat third region may be adjacent to the second region, such that thesecond anchor probe is flanked by the first and third anchor probes.

In some embodiments, sets of anchor and/or sequencing probes willcomprise variable concentrations of each type of probe, and the variableconcentrations may in part depend on the degenerate bases that may becontained in the anchor probes. For example, probes that will have lowerhybridization stability, such as probes with greater numbers of A'sand/or T's, can be present in higher relative concentrations as a way tooffset their lower stabilities. In further embodiments, thesedifferences in relative concentrations are established by preparingsmaller pools of probes independently and then mixing thoseindependently generated pools of probes in the proper amounts.

VIIB(v). Other Sequencing Methods

In one aspect, methods and compositions of the present invention areused in combination with techniques such as those described inWO2007120208, WO2006073504, WO2007133831, and US2007099208, and U.S.Patent Application Nos. 60/992,485; 61/026,337; 61/035,914; 61/061,134;61/116,193; 61/102,586; 12/265,593; 12/266,385; 11/938,096; 11/981,804;No. 11/981,797; 11/981,793; 11/981,767; 11/981,761; 11/981,730;11/981,685; 11/981,661; 11/981,607; 11/981,605; 11/927,388; 11/927,356;11/679,124; 11/541,225; 10/547,214; 11/451,692; and 11/451,691, all ofwhich are incorporated herein by reference in their entirety for allpurposes and in particular for all teachings related to sequencing,particularly sequencing of concatemers.

In a further aspect, sequences of DNBs are identified using sequencingmethods known in the art, including, but not limited to,hybridization-based methods, such as disclosed in Drmanac, U.S. Pat.Nos. 6,864,052; 6,309,824; and 6,401,267; and Drmanac et al, U.S. patentpublication 2005/0191656, and sequencing by synthesis methods, e.g.Nyren et al, U.S. Pat. No. 6,210,891; Ronaghi, U.S. Pat. No. 6,828,100;Ronaghi et al (1998), Science, 281: 363-365; Balasubramanian, U.S. Pat.No. 6,833,246; Quake, U.S. Pat. No. 6,911,345; Li et al, Proc. Natl.Acad. Sci., 100: 414-419 (2003); Smith et al, PCT publication WO2006/074351; and ligation-based methods, e.g. Shendure et al (2005),Science, 309: 1728-1739, Macevicz, U.S. Pat. No. 6,306,597, wherein eachof these references is herein incorporated by reference in its entiretyfor all purposes and in particular teachings regarding the figures,legends and accompanying text describing the compositions, methods ofusing the compositions and methods of making the compositions,particularly with respect to sequencing.

In some embodiments, nucleic acid templates of the invention, as well asDNBs generated from those templates, are used in sequencing by synthesismethods. The efficiency of sequencing by synthesis methods utilizingnucleic acid templates of the invention is increased over conventionalsequencing by synthesis methods utilizing nucleic acids that do notcomprise multiple interspersed adaptors. Rather than a single long read,nucleic acid templates of the invention allow for multiple short readsthat each start at one of the adaptors in the template. Such short readsconsume fewer labeled dNTPs, thus saving on the cost of reagents. Inaddition, sequencing by synthesis reactions can be performed on DNBarrays, which provide a high density of sequencing targets as well asmultiple copies of monomeric units. Such arrays provide detectablesignals at the single molecule level while at the same time providing anincreased amount of sequence information, because most or all of the DNBmonomeric units will be extended without losing sequencing phase. Thehigh density of the arrays also reduces reagent costs—in someembodiments the reduction in reagent costs can be from about 30 to about40% over conventional sequencing by synthesis methods. In someembodiments, the interspersed adaptors of the nucleic acid templates ofthe invention provide a way to combine about two to about ten standardreads if inserted at distances of from about 30 to about 100 bases apartfrom one another. In such embodiments, the newly synthesized strandswill not need to be stripped off for further sequencing cycles, thusallowing the use of a single DNB array through about 100 to about 400sequencing by synthesis cycles.

VIIC. Two-Phase Sequencing

In one aspect, the present invention provides methods for “two-phase”sequencing, which is also referred to herein as “shotgun sequencing”.Such methods are described in U.S. patent application Ser. No.12/325,922, filed Dec. 1, 2008, which is hereby incorporated byreference in its entirety for all purposes and in particular for allteachings related to two-phase or shotgun sequencing.

Generally, two phase-sequencing methods of use in the present inventioncomprise the following steps: (a) sequencing the target nucleic acid toproduce a primary target nucleic acid sequence that comprises one ormore sequences of interest; (b) synthesizing a plurality oftarget-specific oligonucleotides, wherein each of said plurality oftarget-specific oligonucleotides corresponds to at least one of thesequences of interest; (c) providing a library of fragments of thetarget nucleic acid (or constructs that comprise such fragments and thatmay further comprise, for example, adaptors and other sequences asdescribed herein) that hybridize to the plurality of target-specificoligonucleotides; and (d) sequencing the library of fragments (orconstructs that comprise such fragments) to produce a secondary targetnucleic acid sequence. In order to close gaps due to missing sequence orresolve low confidence base calls in a primary sequence of genomic DNA,such as human genomic DNA, the number of target-specificoligonucleotides that are synthesized for these methods may be fromabout ten thousand to about one million; thus the present inventioncontemplates the use of at least about 10,000 target-specificoligonucleotides, or about 25,000, or about 50,000, or about 100,000, orabout 20,000, or about 50,000, or about 100,000, or about 200,000 ormore.

In saying that the plurality of target-specific oligonucleotides“corresponds to” at least one of the sequences of interest, it is meantthat such target-specific oligonucleotides are designed to hybridize tothe target nucleic acid in proximity to, including but not limited to,adjacent to, the sequence of interest such that there is a highlikelihood that a fragment of the target nucleic acid that hybridizes tosuch an oligonucleotides will include the sequence of interest. Suchtarget-specific oligonucleotides are therefore useful for hybrid capturemethods to produce a library of fragments enriched for such sequences ofinterest, as sequencing primers for sequencing the sequence of interest,as amplification primers for amplifying the sequence of interest, or forother purposes.

In shotgun sequencing and other sequencing methods according to thepresent invention, after assembly of sequencing reads, to the skilledperson it is apparent from the assembled sequence that gaps exist orthat there is low confidence in one or more bases or stretches of basesat a particular site in the sequence. Sequences of interest, which mayinclude such gaps, low confidence sequence, or simply differentsequences at a particular location (i.e., a change of one or morenucleotides in target sequence), can also be identified by comparing theprimary target nucleic acid sequence to a reference sequence.

According to one embodiment of such methods sequencing the targetnucleic acid to produce a primary target nucleic acid sequence comprisescomputerized input of sequence readings and computerized assembly of thesequence readings to produce the primary target nucleic acid sequence.In addition, design of the target-specific oligonucleotides can becomputerized, and such computerized synthesis of the target-specificoligonucleotides can be integrated with the computerized input andassembly of the sequence readings and design of the target-specificoligonucleotides. This is especially helpful since the number oftarget-specific oligonucleotides to be synthesized can be in the tens ofthousands or hundreds of thousands for genomes of higher organisms suchas humans, for example. Thus the invention provides automatedintegration of the process of creating the oligonucleotide pool from thedetermined sequences and the regions identified for further processing.In some embodiments, a computer-driven program uses the identifiedregions and determined sequence near or adjacent to such identifiedregions to design oligonucleotides to isolate and/or create newfragments that cover these regions. The oligonucleotides can then beused as described herein to isolate fragments, either from the firstsequencing library, from a precursor of the first sequencing library,from a different sequencing library created from the same target nucleicacid, directly from target nucleic acids, and the like. In furtherembodiments, this automated integration of identifying regions forfurther analysis and isolating/creating the second library defines thesequence of the oligonucleotides within the oligonucleotide pool anddirects synthesis of these oligonucleotides.

In some embodiments of the two phase sequencing methods of theinvention, a releasing process is performed after the hybrid captureprocess, and in other aspects of the technology, an amplificationprocess is performed before the second sequencing process.

In still further embodiments, some or all regions are identified in theidentifying step by comparison of determined sequences with a referencesequence. In some aspects, the second shotgun sequencing library isisolated using a pool of oligonucleotides comprising oligonucleotidesbased on a reference sequence. Also, in some aspects, the pool ofoligonucleotides comprises at least 1000 oligonucleotides of differentsequence, in other aspects, the pool of oligonucleotides comprises atleast 10,000, 25,000, 50,000, 75,000, or 100,000 or moreoligonucleotides of different sequence

In some aspects of the invention, one or more of the sequencingprocesses used in this two-phase sequencing method is performed bysequencing-by-ligation, and in other aspects, one or more of thesequencing processes is performed by sequencing-by-hybridization orsequencing-by-synthesis.

In certain aspects of the invention, between about 1 to about 30% of thecomplex target nucleic acid is identified as having to be re-sequencedin Phase II of the methods, and in other aspects, between about 1 toabout 10% of the complex target nucleic acid is identified as having tobe re-sequenced in Phase II of the methods. In some aspects, coveragefor the identified percentage of complex target nucleic acid is betweenabout 25× to about 100×.

In further aspects, 1 to about 10 target-specific selectionoligonucleotides are defined and synthesized for each target nucleicacid region that is re-sequenced in Phase II of the methods; in otheraspects, about 3 to about 6 target-specific selection oligonucleotidesare defined for each target nucleic acid region that is re-sequenced inPhase II of the methods.

In still further aspects of the technology, the target-specificselection oligonucleotides are identified and synthesized by anautomated process, wherein the process that identifies regions of thecomplex nucleic acid missing nucleic acid sequence or having lowconfidence nucleic acid sequence and defines sequences for thetarget-specific selection oligonucleotides communicates witholigonucleotide synthesis software and hardware to synthesize thetarget-specific selection oligonucleotides. In other aspects of thetechnology, the target-specific selection oligonucleotides are betweenabout 20 and about 30 bases in length, and in some aspects areunmodified.

Not all regions identified for further analysis may actually exist inthe complex target nucleic acid. One reason for predicted lack ofcoverage in a region may be that a region expected to be in the complextarget nucleic acid may actually not be present (e.g., a region may bedeleted or re-arranged in the target nucleic acid), and thus not alloligonucleotides produced from the pool may isolate a fragment forinclusion in the second shotgun sequencing library. In some embodiments,at least one oligonucleotide will be designed and created for eachregion identified for further analysis. In further embodiments, anaverage of three or more oligonucleotides will be provided for eachregion identified for further analysis. It is a feature of the inventionthat the pool of oligonucleotides can be used directly to create thesecond shotgun sequencing library by polymerase extension of theoligonucleotides using templates derived from a target nucleic acid. Itis another feature of the invention that the pool of oligonucleotidescan be used directly to create amplicons via circle dependentreplication using the oligonucleotide pools and circle dependentreplication. It is another feature of the invention that the methodswill provide sequencing information to identify absent regions ofinterest, e.g. predicted regions that were identified for analysis butwhich do not exist, e.g., due to a deletion or rearrangement.

The above described embodiments of the two-phase sequencing method canbe used in combination with any of the nucleic acid constructs andsequencing methods described herein and known in the art.

VIID. SNP Detection

Methods and compositions discussed above can in further embodiments beused to detect specific sequences in nucleic acid constructs such asDNBs. In particular, cPAL methods utilizing sequencing and anchor probescan be used to detect polymorphisms or sequences associated with agenetic mutation, including single nucleotide polymorphisms (SNPs). Forexample, to detect the presence of a SNP, two sets of differentiallylabeled sequencing probes can be used, such that detection of one probeover the other indicates whether a polymorphism present in the sample.Such sequencing probes can be used in conjunction with anchor probes inmethods similar to the cPAL methods described above to further improvethe specificity and efficiency of detection of the SNP.

VIII. Exemplary Embodiments

In one aspect, the present invention provides a method for determining asequence in a target nucleic acid. This method includes the steps of:(a) providing a sequencing template that includes a fragment of thetarget nucleic acid and an adaptor that includes at least a first anchorsite; (b) hybridizing an anchor probe to the anchor site, and the anchorprobe includes a region complementary to the adaptor site and three ormore degenerate bases for binding in the target nucleic acid sequence;(c) hybridizing a pool of sequencing probes for determination of thesequence of one or more nucleotides in a defined position relative tothe adaptor, wherein the sequencing probe is detectably labeled toidentify the presence of a particular base; (d) ligating the anchorprobe and the sequencing probe; and (e) detecting the sequencing probe,thereby determining a sequence in the target nucleic acid.

In a further aspect and in accordance with any of the above, theinvention provides a method of determining the identification of a firstnucleotide at a detection position of a target sequence comprising aplurality of detection positions. This method includes the steps of: (a)providing a surface with a plurality of concatemers, wherein eachconcatemer includes a plurality of monomers and each monomer comprises:(i) a first target domain of the target sequence comprising a first setof target detection positions; (ii) at least a first adaptor comprising:(1) a first anchor site; and (2) a second adjacent anchor site; (b)hybridizing a first anchor probe to the first anchor site; (c)hybridizing a second anchor probe to the second anchor site, wherein thesecond anchor probe also hybridizes to sequences outside the secondanchor site; (d) hybridizing at least a first sequencing probe to thefirst target domain, wherein the first sequencing probe comprises: (i) afirst probe domain complementary to the target domain; (ii) a uniquenucleotide at a first interrogation position; and (iii) a label; underconditions wherein if the unique nucleotide is complementary to thefirst nucleotide, the sequencing probe hybridizes to the concatemer; (e)ligating the anchor probes and the sequencing probe; and (f) identifyingthe first nucleotide.

In one embodiment, and in accordance with any of the above, the presentinvention provides a method of determining the identification of a firstnucleotide at a detection position of a target sequence in which a setof sequencing probes are contacted with a surface comprising a pluralityof concatemers. In this embodiment, each sequencing probe includes: (a)a first probe domain complementary to the target domain; (b) a uniquenucleotide at a first interrogation position; and (c) a label; whereineach label of the set corresponds to the unique nucleotide.

In a further embodiment, and in accordance with any of the above, eachof the monomers in a concatemer comprises a plurality of adaptors.

In a still further embodiment and in accordance with any of the above,at least one of the adaptors in a concatemer includes at least one TypeIIs endonuclease recognition site.

In a still further embodiment and in accordance with any of the above,the steps of hybridizing a first anchor probe to the first anchor site;hybridizing a second anchor probe to a second anchor site; hybridizingat least a first sequencing probe to the first target domain; andligating the anchor probes and the sequencing probe are repeated toidentify a second nucleotide at a second detection position.

In a further embodiment and in accordance with any of the above, thesecond anchor probe includes a set of second anchor probes comprising atleast three degenerate bases that hybridize to sequences outside thesecond anchor site.

In a still further embodiment and in accordance with any of the above,the second anchor probe comprises at least one terminus that isselectively activatable for ligation.

In a still further embodiment and in accordance with any of the above,the surface with a plurality of concatemers is a functionalized surface.In a still further embodiment, the surface is functionalized withfunctional moieties selected from a group including amines, silanes, andhydroxyls.

In a still further embodiment and in accordance with any of the above,the surface comprises a plurality of spatially distinct regionscomprising the immobilized concatemers.

In a further embodiment and in accordance with any of the above, theconcatemers are immobilized on the surface using capture probes.

In a still further embodiment and in accordance with any of the above,genomic nucleic acids are fragmented to form target sequences.

In a still further embodiment and in accordance with any of the above,the target sequence is a genomic nucleic acid sequence.

In a still further embodiment and in accordance with any of the above,the genomic nucleic acid sequences are human.

In one aspect and in accordance with any of the above, the presentinvention provides kits for use with sequencing templates that caninclude the sets of probes described herein. In general, kits of theinvention can include anchor probe pairs, anchor probe pairs and anadditional anchor probe adjacent to a target nucleic acid in a template,and sequencing probes for base determination at specific positions inthe nucleic acid template. Such kits may further comprise adaptors foruse in the generation of nucleic acid templates for use in the presentmethods.

In one aspect and in accordance with any of the above, the presentinvention provides a nucleic acid sequencing system that comprises 10pools of labeled or tagged probes, sets of anchor probes comprising 4 ormore probes of different sequences, sets of anchor probes with 3 or moredegenerate bases, and ligase. In a further embodiment, the nucleic acidsequencing system will further comprise an agent for denaturing anchorprobes, sequencing probes, and ligated sequencing and anchor probes froma nucleic acid template.

EXAMPLES Example 1 Producing DNBs

The following are exemplary protocols for producing DNBs (also referredto herein as “amplicons”) from nucleic acid templates of the inventioncomprising target nucleic acids interspersed with one or more adaptors.Single-stranded linear nucleic acid templates are first subjected toamplification with a phosphorylated 5′ primer and a biotinylated 3′primer, resulting in a double-stranded linear nucleic acid templatestagged with biotin.

First, streptavidin magnetic beads were prepared by resuspendingMagPrep-Streptavidin beads (Novagen Part. No. 70716-3) in 1× beadbinding buffer (150 mM NaCl and 20 mM Tris, pH 7.5 in nuclease freewater) in nuclease-free microfuge tubes. The tubes were placed in amagnetic tube rack, the magnetic particles were allowed to clear, andthe supernatant was removed and discarded. The beads were then washedtwice in 800 μl 1× bead binding buffer, and resuspended in 80 μl 1× beadbinding buffer. Amplified nucleic acid templates (also referred toherein as “library constructs”) from the PCR reaction were brought up to60 μl volume, and 20 μl 4× bead binding buffer was added to the tube.The nucleic acid templates were then added to the tubes containing theMagPrep beads, mixed gently, incubated at room temperature for 10minutes and the MagPrep beads were allowed to clear. The supernatant wasremoved and discarded. The MagPrep beads (mixed with the amplifiedlibrary constructs) were then washed twice in 800 μl 1× bead bindingbuffer. After washing, the MagPrep beads were resuspended in 80 μl 0.1NNaOH, mixed gently, incubated at room temperature and allowed to clear.The supernatant was removed and added to a fresh nuclease-free tube. 4μl 3M sodium acetate (pH 5.2) was added to each supernatant and mixedgently.

Next, 420 μl of PBI buffer (supplied with QIAprep PCR Purification Kits)was added to each tube, the samples were mixed and then were applied toQIAprep Miniprep columns (Qiagen Part No. 28106) in 2 ml collectiontubes and centrifuged for 1 minutes at 14,000 rpm. The flow through wasdiscarded, and 0.75 ml PE buffer (supplied with QIAprep PCR PurificationKits) was added to each column, and the column was centrifuged for anadditional 1 minute. Again the flow through was discarded. The columnwas transferred to a fresh tube and 50 μl of EB buffer (supplied withQIAprep PCR Purification Kits) was added. The columns were spun at14,000 for 1 minute to elute the single-stranded nucleic acid templates.The quantity of each sample was then measured.

Circularization of single-stranded templates using CircLigase: First, 10μmol of the single-stranded linear nucleic acid templates wastransferred to a nuclease-free PCR tube. Nuclease free water was addedto bring the reaction volume to 30 μl, and the samples were kept on ice.Next, 4 μl 10× CircLigase Reaction Buffer (Epicentre Part. No. CL4155K),2 μl 1 mM ATP, 2 μl 50 mM MnCl₂, and 2 μl CircLigase (100 U/μl)(collectively, 4× CircLigase Mix) were added to each tube, and thesamples were incubated at 60° C. for 5 minutes. Another 10 μl of 4×CircLigase Mix was added was added to each tube and the samples wereincubated at 60° for 2 hours, 80° C. for 20 minutes, then 4° C. Thequantity of each sample was then measured.

Removal of residual linear DNA from CircLigase reactions by Exonucleasedigestion. First, 30 μl of each CircLigase sample was added to anuclease-free PCR tube, then 3 μl water, 4 μl 10× Exonuclease ReactionBuffer (New England Biolabs Part No. B0293S), 1.5 μl Exonuclease I (20U/μl, New England Biolabs Part No. M0293L), and 1.5 μl Exonuclease III(100 U/μl, New England Biolabs Part No. M0206L) were added to eachsample. The samples were incubated at 37° C. for 45 minutes. Next, 75 mMEDTA, ph 8.0 was added to each sample and the samples were incubated at85° C. for 5 minutes, then brought down to 4° C. The samples were thentransferred to clean nuclease-free tubes. Next, 500 μl of PN buffer(supplied with QIAprep PCR Purification Kits) was added to each tube,mixed and the samples were applied to QIAprep Miniprep columns (QiagenPart No. 28106) in 2 ml collection tubes and centrifuged for 1 minute at14,000 rpm. The flow through was discarded, and 0.75 ml PE buffer(supplied with QIAprep PCR Purification Kits) was added to each column,and the column was centrifuged for an additional 1 minute. Again theflow through was discarded. The column was transferred to a fresh tubeand 40 μl of EB buffer (supplied with QIAprep PCR Purification Kits) wasadded. The columns were spun at 14,000 for 1 minute to elute thesingle-stranded library constructs. The quantity of each sample was thenmeasured.

Circle dependent replication for DNB production: The nucleic acidtemplates were subjected to circle dependent replication to create DNBscomprising concatamers of target nucleic acid and adaptor sequences. 40fmol of exonuclease-treated single-stranded circles were added tonuclease-free PCR strip tubes, and water was added to bring the finalvolume to 10.0. μl. Next, 10 μl of 2× Primer Mix (7 μl water, 2 μl10×phi29 Reaction Buffer (New England Biolabs Part No. B0269S), and 1 μlprimer (2 μM)) was added to each tube and the tubes were incubated atroom temperature for 30 minutes. Next, 20 μl of phi 29 Mix (14 μl water,2 μl 10×phi29 Reaction Buffer (New England Biolabs Part No. B0269S), 3.2dNTP mix (2.5 mM of each dATP, dCTP, dGTP and dTTP), and 0.8 μl phi29DNA polymerase (10 U/μl, New England Biolabs Part No. M0269S)) was addedto each tube. The tubes were then incubated at 30° C. for 120 minutes.The tubes were then removed, and 75 mM EDTA, pH 8.0 was added to eachsample. The quantity of circle dependent replication product was thenmeasured.

Determining DNB quality: Once the quantity of the DNBs was determined,the quality of the DNBs was assessed by looking at color purity. TheDNBs were suspended in amplicon dilution buffer (0.8×phi29 ReactionBuffer (New England Biolabs Part No. B0269S) and 10 mM EDTA, pH 8.0),and various dilutions were added into lanes of a flowslide and incubatedat 30° C. for 30 minutes. The flowslides were then washed with bufferand a probe solution containing four different random 12-mer probeslabeled with Cy5, Texas Red, FITC or Cy3 was added to each lane. Theflow slides were transferred to a hot block pre-heated to 30° C. andincubated at 30° C. for 30 minutes. The flow slides were then imagedusing Imager 3.2.1.0 software. The quantity of circle dependentreplication product was then measured.

Example 2 Single and Double c-PAL

Different lengths of fully degenerate second anchor probes were testedin a two anchor probe detection system. The combinations used were: 1)standard one anchor ligation using an anchor that binds to the adaptoradjacent to the target nucleic acid and a 9-mer sequencing probe,reading at position 4 from the adaptor 2) two anchor ligation using thesame first anchor and a second anchor comprising a degenerate five-merand a 9-mer sequencing probe, reading at position 9 from the adaptor; 3)two anchor ligation using the same first anchor and a second anchorcomprising a degenerate six-mer and a 9-mer sequencing probe, reading atposition 10 from the adaptor; and 4) two anchor ligation using the samefirst anchor and a second anchor comprising a degenerate eight-mer and a9-mer sequencing probe, reading at position 12 from the adaptor. 1 μM ofa first anchor probe and 6 μM of a degenerate second anchor probe werecombined with T4 DNA ligase in a ligase reaction buffer and applied tothe surface of the reaction slide for 30 minutes, after which time theunreacted probes and reagents were washed from the slide. A secondreaction mix containing ligase and fluorescent probes of the type 5′FI-NNNNNBNNN or 5′ FI-NNBNNNNNN 5′ FI-NNNBNNNNN 5′ FI-NNNNBNNNN wasintroduced. FI represents one of four fluorophores, N represents any oneof the four bases A, G, C, or T introduced at random, and B representsone of the four bases A, G, C, or T specifically associated with thefluorophore. After ligation for 1 hr the unreacted probes and reagentswere washed from the slide and the fluorescence associated with each DNAtarget was assayed.

FIG. 27 demonstrates signal intensities associated with the differentlength degenerate second anchor probes in the systems, with intensitiesdecreasing with increased second anchor probe length. As seen in FIG.28, the fit scores for such intensities also decreased with the lengthof the degenerate second anchor, but still generated reasonable fitscores through the base 10 read.

The effect of time using the one anchor probe method and the two anchorprobe method is illustrated in FIGS. 29 and 30. The standard anchor anddegenerate five-mer were both used with a 9-mer sequencing probe to readpositions 4 and 9 from the adaptor, respectively. Although the intensitylevels differed more in the two anchor probe method, both the standardone anchor method and the two anchor probe methods at both timesdemonstrated comparable fit scores, each being over 0.8.

Effect of degenerate second anchor probe length on intensity and fitscore: Different combinations of first and second anchor probes withvarying second anchor probe length and composition were used to comparethe effect of the degenerate anchor probe on signal intensity and fitscore when used to identify a base 5′ of the adaptor. Standard oneanchor methods were compared to signal intensities and fit scores usingtwo anchor probe methods with either partially degenerate probes havingsome region of complementarity to the adaptor, or fully degeneratesecond anchor probes. Degenerate second anchor probes of five-mers tonine-mers were used at one concentration, and two of these—the 6-mer andthe seven-mer, were also tested at 4× concentration. Second anchorprobes comprising two nucleotides of adaptor complementarity anddifferent lengths of degenerate nucleotides at their 3′ end were alsotested at the first concentration. Each of the reactions utilized a sameset of four sequencing probes for identification of the nucleotidepresent at the read position in the target nucleic acid.

The combinations used in the experiments are as follows:

-   -   Reaction 1:1 μM of a 12 base first anchor probe        -   No second anchor probe        -   Read position: 2 nt from the adaptor end    -   Reaction 2: 1 μM of a 12 base first anchor probe        -   20 μM of 5 degenerate base second anchor probe        -   Read position: 7 nt from the adaptor end    -   Reaction 3: 1 μM of a 12 base first anchor probe        -   20 μM of a 6 degenerate base second anchor probe        -   Read position: 8 nt from the adaptor end    -   Reaction 4: 1 μM of a 12 base first anchor probe        -   20 μM of a 7 degenerate base second anchor probe        -   Read position: 9 nt from the adaptor end    -   Reaction 5: 1 μM of a 12 base first anchor probe        -   20 μM of an 8 degenerate base second anchor probe        -   Read position: 10 nt from the adaptor end    -   Reaction 6: 1 μM of a 12 base first anchor probe        -   20 μM of a 9 degenerate base second anchor probe        -   Read position: lint from the adaptor end    -   Reaction 7: 1 μM of a 12 base first anchor probe        -   80 μM of a 6 degenerate base second anchor probe        -   Read position: 8 nt from the adaptor end    -   Reaction 8: 1 μM of a 12 base first anchor probe        -   80 μM of a 7 degenerate base second anchor probe        -   Read position: 9 nt from the adaptor end    -   Reaction 9: 1 μM of a 12 base first anchor probe        -   20 μM of a 6 nt second anchor probe (4 degenerate bases-2            known bases)        -   Read position: 6 nt from the adaptor end    -   Reaction 10:1 μM of a 12 base first anchor probe        -   20 μM of a 7 nt second anchor probe (5 degenerate bases-2            known bases)        -   Read position: 7 nt from the adaptor end    -   Reaction 11: 1 μM of a 12 base first anchor probe        -   20 μM of an 8 nt second anchor probe (6 degenerate bases-2            known bases)        -   Read position: 8 nt from the adaptor end

FIGS. 31 and 32 illustrate the results of the different combinations ofanchor probes and sequencing probes. The length of the degenerate secondanchor probe was shown to be best using a six-mer, whether it wascompletely degenerate or partially degenerate. The signal intensitiesusing a fully degenerate six-mer at a higher concentration showed signalintensities similar to that of the partially degenerate six-mer (FIG.31). All data had fairly good fit scores (see FIG. 32) except Reaction 6using the longest of the second anchors, which also displayed the lowestintensity scores of the reactions performed (FIG. 31).

Effect of first anchor probe length on intensity and fit score:Different combinations of first and second anchor probes with varyingfirst anchor probe length were used to compare the effect of the firstanchor probe length on signal intensity and fit score when used toidentify a base 3′ of the adaptor. Standard one anchor methods werecompared to signal intensities and fit scores using two anchor probemethods with either partially degenerate probes having some region ofcomplementarity to the adaptor, or fully degenerate second anchorprobes. Each of the reactions utilized a same set of four sequencingprobes for identification of the nucleotide present at the read positionin the target nucleic acid. The combinations used in the experiment areas follows:

-   -   Reaction 1:1 μM of a 12 base first anchor probe        -   No second anchor probe        -   Read position: 5 nt from the adaptor end    -   Reaction 2: 1 μM of a 12 base first anchor probe        -   20 μM of 5 degenerate base second anchor probe        -   Read position: 10 nt from the adaptor end    -   Reaction 3: 1 μM of a 10 base first anchor probe        -   20 μM of a 7 nt second anchor probe (5 degenerate bases-2            known bases)        -   Read position: 10 nt from the adaptor end    -   Reaction 4: 1 μM of a 13 base first anchor probe        -   20 μM of a 7 degenerate base second anchor probe        -   Read position: 12 nt from the adaptor end    -   Reaction 5: 1 μM of a 12 base first anchor probe        -   20 μM of an 7 degenerate base second anchor probe        -   Read position: 12 nt from the adaptor end    -   Reaction 6: 1 μM of a 11 base first anchor probe        -   20 μM of a 7 degenerate base second anchor probe        -   Read position: 12 nt from the adaptor end    -   Reaction 7: 1 μM of a 10 base first anchor probe        -   20 μM of a 7 degenerate base second anchor probe        -   Read position: 12 nt from the adaptor end    -   Reaction 8: 1 μM of a 9 base first anchor probe        -   80 μM of a 7 degenerate base second anchor probe        -   Read position: 12 nt from the adaptor end

The signal intensity (FIG. 33) and fit scores (FIG. 34) observed show anoptimum intensity resulting from use of the longer first anchor probes,which in part may be due to the greater meting temperature the longerprobes provide to the combined anchor probe.

Effect of kinase incubations on intensity and fit score using two anchorprimer methods: The reactions as described above were performed atdifferent temperatures using 1 μM of a 10 base first anchor probe, 20 μMof a 7-mer second anchor probe, and sequencing probe with the structureFluor-NNNNBNNNN to read position 10 from the adaptor in the presence ofa kinase at 1Unit/ml for a period of three days. A reaction with a15-mer first anchor and the sequencing probe served as a positivecontrol. Results are as shown in FIGS. 35 and 36. Although the kinasedid have an effect on signal intensities as compared to the control, therange did not change from 4° C. to 37° C., and fit scores remainedequivalent with the control. The temperature at which the kinaseincubation did have an impact is 42° C., which also displayed a poor fitwith the data.

The minimum time needed to kinase was then examined using the sameprobes and conditions as described above. As shown in FIGS. 37 and 38,kinase incubation of five minutes or above resulting in effectivelyequivalent signal intensities and fit score.

The present specification provides a complete description of themethodologies, systems and/or structures and uses thereof in exampleaspects of the presently-described technology. Although various aspectsof this technology have been described above with a certain degree ofparticularity, or with reference to one or more individual aspects,those skilled in the art could make numerous alterations to thedisclosed aspects without departing from the spirit or scope of thetechnology hereof. Since many aspects can be made without departing fromthe spirit and scope of the presently described technology, theappropriate scope resides in the claims hereinafter appended. Otheraspects are therefore contemplated. Furthermore, it should be understoodthat any operations may be performed in any order, unless explicitlyclaimed otherwise or a specific order is inherently necessitated by theclaim language. It is intended that all matter contained in the abovedescription and shown in the accompanying drawings shall be interpretedas illustrative only of particular aspects and are not limiting to theembodiments shown. Unless otherwise clear from the context or expresslystated, any concentration values provided herein are generally given interms of admixture values or percentages without regard to anyconversion that occurs upon or following addition of the particularcomponent of the mixture. To the extent not already expresslyincorporated herein, all published references and patent documentsreferred to in this disclosure are incorporated herein by reference intheir entirety for all purposes. Changes in detail or structure may bemade without departing from the basic elements of the present technologyas defined in the following claims.

1. A method of determining the identification of a first nucleotide at adetection position of a target sequence comprising a plurality ofdetection positions, said method comprising: (a) providing a surfacecomprising a plurality of concatemers, wherein each concatemer comprisesa plurality of monomers and each monomer comprises: i) a first targetdomain of said target sequence comprising a first set of targetdetection positions; ii) at least a first adaptor comprising: 1) a firstanchor site; and 2) a second adjacent anchor site; b) hybridizing afirst anchor probe to said first anchor site; c) hybridizing a secondanchor probe to said second anchor site, wherein said second anchorprobe also hybridizes to sequences outside said second anchor site; d)hybridizing at least a first sequencing probe to said first targetdomain, wherein said first sequencing probe comprises: i) a first probedomain complementary to said target domain; ii) a unique nucleotide at afirst interrogation position; and iii) a label; under conditions whereinif said unique nucleotide is complementary to said first nucleotide,said sequencing probe hybridizes to said concatemer; and e) ligatingsaid anchor probes and said sequencing probe; f) identifying said firstnucleotide.
 2. A method according to claim 1 wherein a set of sequencingprobes are contacted with said surface, each sequencing probecomprising: a) a first probe domain complementary to said target domain;b) a unique nucleotide at a first interrogation position; and c) alabel; wherein each label of said set corresponds to said uniquenucleotide.
 3. A method according to claim 1 wherein each of saidmonomers comprises a plurality of adaptors.
 4. A method according toclaim 3 wherein at least one of said adaptors comprises at least oneType IIs endonuclease recognition site.
 5. A method according to claim 1wherein steps b)-e) are repeated to identify a second nucleotide at asecond detection position.
 6. A method according to claim 1, whereinsaid second anchor probe comprises a set of second anchor probescomprising at least three degenerate bases that hybridizes to saidsequences outside said second anchor site.
 7. A method according toclaim 1, wherein said second anchor probe comprises at least oneterminus that is selectively activatable for ligation.
 8. A methodaccording to claim 1 wherein said surface is functionalized.
 9. A methodaccording to claim 8 wherein said functionalized surface comprisesfunctional moieties selected from the group consisting of amines,silanes, and hydroxyls.
 10. A method according to claim 1 wherein saidsurface comprises a plurality of spatially distinct regions comprisingsaid immobilized concatemers.
 11. A method according to claim 1 whereinsaid concatemers are immobilized on said surface using capture probes.12. A method according to claim 1 further comprising fragmenting genomicnucleic acid to form target sequences.
 13. A method according to claim 1wherein said target sequence is a genomic nucleic acid sequence.
 14. Amethod according to claim 13 wherein said genomic nucleic acid sequencesare human.
 15. A method of determining the identification of a firstnucleotide at a detection position of a target sequence comprising aplurality of detection positions, said method comprising: (a) providinga surface comprising a plurality of concatemers, wherein each concatemercomprises a plurality of monomers and each monomer comprises: i) a firsttarget domain of said target sequence comprising a first set of targetdetection positions; ii) at least a first adaptor comprising: 1) a firstanchor site; and 2) a second adjacent anchor site; b) hybridizing afirst anchor probe to said first anchor site; c) hybridizing a secondanchor probe to said second anchor site, wherein said second anchorprobe also hybridizes to sequences outside said second anchor site; d)hybridizing at least a first sequencing probe to said first targetdomain, wherein said first sequencing probe comprises: i) a first probedomain complementary to said target domain; ii) a unique nucleotide at afirst interrogation position; and iii) a label; under conditions whereinif said unique nucleotide is complementary to a first nucleotide in saidfirst set of target detection positions, said sequencing probehybridizes to said concatemer; e) ligating said anchor probes and saidsequencing probe to form a probe ligation product; and then f) detectingsaid probe ligation product thereby identifying said first nucleotide.